Revisions to How to remedy a DESeq2 collapsing technical replicates error?

Removed `cell_type` info from my `coldata` to better match the example output (especially because that column did not affect the outcome of the replicate collapsing).

Source Link

edited Jan 13, 2022 at 20:32

Gawain

335
1
10

> head(cts)
            KO1_P1_L001.Counts KO1_P1_L002.Counts KO1_P2_L001.Counts KO1_P2_L002.Counts KO1_P3_L001.Counts KO1_P3_L002.Counts KO2_P1_L001.Counts KO2_P1_L002.Counts KO2_P2_L001.Counts KO2_P2_L002.Counts KO2_P3_L001.Counts KO2_P3_L002.Counts WT_P1_L001.Counts WT_P1_L002.Counts WT_P2_L001.Counts WT_P2_L002.Counts WT_P3_L001.Counts WT_P3_L002.Counts
DDX11L1                      1                  0                  1                  1                  2                  1                  0                  1                  2                  1                  3                  1                 7                 2                 1                 1                 0                 0
WASH7P                     124                144                128                151                102                118                 39                 41                103                 87                105                106               125               120                13                26               104               136
MIR6859-1                    8                  6                  4                  5                  4                  6                  2                  2                  7                  2                  7                  6                 6                 6                 2                 2                 2                 9
MIR1302-2HG                  1                  4                  0                  0                  0                  2                  2                  2                  2                  2                  0                  4                 1                 2                 0                 3                 2                 2
MIR1302-2                    0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                 0                 0                 0                 0                 0                 0
FAM138A                      0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                 0                 0                 0                 0                 0                 0

> print(coldata)
                   cell_type condition sample           run
KO1_P1_L001.Counts     human    longKO     l1  long_P1_L001
KO1_P1_L002.Counts     human    longKO     l1  long_P1_L002
KO1_P2_L001.Counts     human    longKO     l2  long_P2_L001
KO1_P2_L002.Counts     human    longKO     l2  long_P2_L002
KO1_P3_L001.Counts     human    longKO     l3  long_P3_L001
KO1_P3_L002.Counts     human    longKO     l3  long_P3_L002
KO2_P1_L001.Counts     human   shortKO     s1 short_P1_L001
KO2_P1_L002.Counts     human   shortKO     s1 short_P1_L002
KO2_P2_L001.Counts     human   shortKO     s2 short_P2_L001
KO2_P2_L002.Counts     human   shortKO     s2 short_P2_L002
KO2_P3_L001.Counts     human   shortKO     s3 short_P3_L001
KO2_P3_L002.Counts     human   shortKO     s3 short_P3_L002
WT_P1_L001.Counts      human        WT     w1    wt_P1_L001
WT_P1_L002.Counts      human        WT     w1    wt_P1_L002
WT_P2_L001.Counts      human        WT     w2    wt_P2_L001
WT_P2_L002.Counts      human        WT     w2    wt_P2_L002
WT_P3_L001.Counts      human        WT     w3    wt_P3_L001
WT_P3_L002.Counts      human        WT     w3    wt_P3_L002

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> colData(ddsColl)
DataFrame with 9 rows and 54 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0)

> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

> head(cts)
            KO1_P1_L001.Counts KO1_P1_L002.Counts KO1_P2_L001.Counts KO1_P2_L002.Counts KO1_P3_L001.Counts KO1_P3_L002.Counts KO2_P1_L001.Counts KO2_P1_L002.Counts KO2_P2_L001.Counts KO2_P2_L002.Counts KO2_P3_L001.Counts KO2_P3_L002.Counts WT_P1_L001.Counts WT_P1_L002.Counts WT_P2_L001.Counts WT_P2_L002.Counts WT_P3_L001.Counts WT_P3_L002.Counts
DDX11L1                      1                  0                  1                  1                  2                  1                  0                  1                  2                  1                  3                  1                 7                 2                 1                 1                 0                 0
WASH7P                     124                144                128                151                102                118                 39                 41                103                 87                105                106               125               120                13                26               104               136
MIR6859-1                    8                  6                  4                  5                  4                  6                  2                  2                  7                  2                  7                  6                 6                 6                 2                 2                 2                 9
MIR1302-2HG                  1                  4                  0                  0                  0                  2                  2                  2                  2                  2                  0                  4                 1                 2                 0                 3                 2                 2
MIR1302-2                    0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                 0                 0                 0                 0                 0                 0
FAM138A                      0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                 0                 0                 0                 0                 0                 0

> print(coldata)
                   cell_type condition sample           run
KO1_P1_L001.Counts     human    longKO     l1  long_P1_L001
KO1_P1_L002.Counts     human    longKO     l1  long_P1_L002
KO1_P2_L001.Counts     human    longKO     l2  long_P2_L001
KO1_P2_L002.Counts     human    longKO     l2  long_P2_L002
KO1_P3_L001.Counts     human    longKO     l3  long_P3_L001
KO1_P3_L002.Counts     human    longKO     l3  long_P3_L002
KO2_P1_L001.Counts     human   shortKO     s1 short_P1_L001
KO2_P1_L002.Counts     human   shortKO     s1 short_P1_L002
KO2_P2_L001.Counts     human   shortKO     s2 short_P2_L001
KO2_P2_L002.Counts     human   shortKO     s2 short_P2_L002
KO2_P3_L001.Counts     human   shortKO     s3 short_P3_L001
KO2_P3_L002.Counts     human   shortKO     s3 short_P3_L002
WT_P1_L001.Counts      human        WT     w1    wt_P1_L001
WT_P1_L002.Counts      human        WT     w1    wt_P1_L002
WT_P2_L001.Counts      human        WT     w2    wt_P2_L001
WT_P2_L002.Counts      human        WT     w2    wt_P2_L002
WT_P3_L001.Counts      human        WT     w3    wt_P3_L001
WT_P3_L002.Counts      human        WT     w3    wt_P3_L002

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> colData(ddsColl)
DataFrame with 9 rows and 5 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0)

> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

> head(cts)
            KO1_P1_L001.Counts KO1_P1_L002.Counts KO1_P2_L001.Counts KO1_P2_L002.Counts KO1_P3_L001.Counts KO1_P3_L002.Counts KO2_P1_L001.Counts KO2_P1_L002.Counts KO2_P2_L001.Counts KO2_P2_L002.Counts KO2_P3_L001.Counts KO2_P3_L002.Counts WT_P1_L001.Counts WT_P1_L002.Counts WT_P2_L001.Counts WT_P2_L002.Counts WT_P3_L001.Counts WT_P3_L002.Counts
DDX11L1                      1                  0                  1                  1                  2                  1                  0                  1                  2                  1                  3                  1                 7                 2                 1                 1                 0                 0
WASH7P                     124                144                128                151                102                118                 39                 41                103                 87                105                106               125               120                13                26               104               136
MIR6859-1                    8                  6                  4                  5                  4                  6                  2                  2                  7                  2                  7                  6                 6                 6                 2                 2                 2                 9
MIR1302-2HG                  1                  4                  0                  0                  0                  2                  2                  2                  2                  2                  0                  4                 1                 2                 0                 3                 2                 2
MIR1302-2                    0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                 0                 0                 0                 0                 0                 0
FAM138A                      0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                  0                 0                 0                 0                 0                 0                 0

> print(coldata)
                   condition sample           run
KO1_P1_L001.Counts    longKO     l1  long_P1_L001
KO1_P1_L002.Counts    longKO     l1  long_P1_L002
KO1_P2_L001.Counts    longKO     l2  long_P2_L001
KO1_P2_L002.Counts    longKO     l2  long_P2_L002
KO1_P3_L001.Counts    longKO     l3  long_P3_L001
KO1_P3_L002.Counts    longKO     l3  long_P3_L002
KO2_P1_L001.Counts   shortKO     s1 short_P1_L001
KO2_P1_L002.Counts   shortKO     s1 short_P1_L002
KO2_P2_L001.Counts   shortKO     s2 short_P2_L001
KO2_P2_L002.Counts   shortKO     s2 short_P2_L002
KO2_P3_L001.Counts   shortKO     s3 short_P3_L001
KO2_P3_L002.Counts   shortKO     s3 short_P3_L002
WT_P1_L001.Counts         WT     w1    wt_P1_L001
WT_P1_L002.Counts         WT     w1    wt_P1_L002
WT_P2_L001.Counts         WT     w2    wt_P2_L001
WT_P2_L002.Counts         WT     w2    wt_P2_L002
WT_P3_L001.Counts         WT     w3    wt_P3_L001
WT_P3_L002.Counts         WT     w3    wt_P3_L002

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> colData(ddsColl)
DataFrame with 9 rows and 4 columns
   condition      sample           run               runsCollapsed
    <factor> <character>   <character>                 <character>
l1    longKO          l1  long_P1_L001   long_P1_L001,long_P1_L002
l2    longKO          l2  long_P2_L001   long_P2_L001,long_P2_L002
l3    longKO          l3  long_P3_L001   long_P3_L001,long_P3_L002
s1   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1        WT          w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2        WT          w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3        WT          w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0)

> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

Removed the commands referring to the creation of the `cts` and `coldata` objects since I have provided the `cts` and `coldata` "input files".

Source Link

edited Jan 13, 2022 at 17:30

Gawain

335
1
10

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> dds
class: DESeqDataSet 
dim: 59368 18 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(18): KO1_P1_L001.Counts KO1_P1_L002.Counts ... WT_P3_L001.Counts WT_P3_L002.Counts
colData names(4): cell_type condition sample run

> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> ddsColl
class: DESeqDataSet 
dim: 59368 9 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(9): l1 l2 ... w2 w3
colData names(5): cell_type condition sample run runsCollapsed

> colData(ddsColl)
DataFrame with 9 rows and 5 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0) 

> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

From the output of dds and ddsColl, it seems the number of columns decreased from 18 to 9, as expected. The only difference I see between my DESeq2 workflow output is the result of matchFirstLevel (see below for expected result). Why might this be for my dataset, but not the example dataset?

> dds <- makeExampleDESeqDataSet(m=12)
> dds$sample <- factor(sample(paste0("sample",rep(1:9, c(2,1,1,2,1,1,2,1,1)))))
> dds$run <- paste0("run",1:12)
> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> colData(ddsColl)
DataFrame with 9 rows and 4 columns
        condition   sample         run runsCollapsed
         <factor> <factor> <character>   <character>
sample1         B  sample1       run10   run10,run11
sample2         A  sample2        run5          run5
sample3         A  sample3        run6          run6
sample4         A  sample4        run1     run1,run4
sample5         B  sample5        run7          run7
sample6         B  sample6        run9          run9
sample7         A  sample7        run3    run3,run12
sample8         B  sample8        run8          run8
sample9         A  sample9        run2          run2
> colnames(ddsColl)
[1] "sample1" "sample2" "sample3" "sample4" "sample5" "sample6" "sample7" "sample8" "sample9"
> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE 

> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> dds
class: DESeqDataSet 
dim: 59368 18 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(18): KO1_P1_L001.Counts KO1_P1_L002.Counts ... WT_P3_L001.Counts WT_P3_L002.Counts
colData names(4): cell_type condition sample run

> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> ddsColl
class: DESeqDataSet 
dim: 59368 9 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(9): l1 l2 ... w2 w3
colData names(5): cell_type condition sample run runsCollapsed

> colData(ddsColl)
DataFrame with 9 rows and 5 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0)
> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

The only difference I see between my DESeq2 workflow output is the result of matchFirstLevel (see below for expected result). Why might this be for my dataset, but not the example dataset?

> dds <- makeExampleDESeqDataSet(m=12)
> dds$sample <- factor(sample(paste0("sample",rep(1:9, c(2,1,1,2,1,1,2,1,1)))))
> dds$run <- paste0("run",1:12)
> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> colData(ddsColl)
DataFrame with 9 rows and 4 columns
        condition   sample         run runsCollapsed
         <factor> <factor> <character>   <character>
sample1         B  sample1       run10   run10,run11
sample2         A  sample2        run5          run5
sample3         A  sample3        run6          run6
sample4         A  sample4        run1     run1,run4
sample5         B  sample5        run7          run7
sample6         B  sample6        run9          run9
sample7         A  sample7        run3    run3,run12
sample8         B  sample8        run8          run8
sample9         A  sample9        run2          run2
> colnames(ddsColl)
[1] "sample1" "sample2" "sample3" "sample4" "sample5" "sample6" "sample7" "sample8" "sample9"
> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE
> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> colData(ddsColl)
DataFrame with 9 rows and 5 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0) 

> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

From the output of dds and ddsColl, it seems the number of columns decreased from 18 to 9, as expected. The only difference I see between my DESeq2 workflow output is the result of matchFirstLevel (see below for expected result). Why might this be for my dataset, but not the example dataset?

> dds <- makeExampleDESeqDataSet(m=12)
> dds$sample <- factor(sample(paste0("sample",rep(1:9, c(2,1,1,2,1,1,2,1,1)))))
> dds$run <- paste0("run",1:12)
> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> colData(ddsColl)
DataFrame with 9 rows and 4 columns
        condition   sample         run runsCollapsed
         <factor> <factor> <character>   <character>
sample1         B  sample1       run10   run10,run11
sample2         A  sample2        run5          run5
sample3         A  sample3        run6          run6
sample4         A  sample4        run1     run1,run4
sample5         B  sample5        run7          run7
sample6         B  sample6        run9          run9
sample7         A  sample7        run3    run3,run12
sample8         B  sample8        run8          run8
sample9         A  sample9        run2          run2

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE 

> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))

Removed the commands referring to the creation of the `cts` and `coldata` objects since I have provided the `cts` and `coldata` "input files".

Source Link

edited Jan 13, 2022 at 17:22

Gawain

335
1
10

> cts <- read.table("counts.txt", header=T, sep="\t", row.names="Geneid")
> coldata <- read.csv(file="annotationFile.csv", sep=",", row.names=1)

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> dds
class: DESeqDataSet 
dim: 59368 18 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(18): KO1_P1_L001.Counts KO1_P1_L002.Counts ... WT_P3_L001.Counts WT_P3_L002.Counts
colData names(4): cell_type condition sample run

> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> ddsColl
class: DESeqDataSet 
dim: 59368 9 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(9): l1 l2 ... w2 w3
colData names(5): cell_type condition sample run runsCollapsed

> colData(ddsColl)
DataFrame with 9 rows and 5 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0)
> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

> cts <- read.table("counts.txt", header=T, sep="\t", row.names="Geneid")
> coldata <- read.csv(file="annotationFile.csv", sep=",", row.names=1)

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> dds
class: DESeqDataSet 
dim: 59368 18 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(18): KO1_P1_L001.Counts KO1_P1_L002.Counts ... WT_P3_L001.Counts WT_P3_L002.Counts
colData names(4): cell_type condition sample run

> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> ddsColl
class: DESeqDataSet 
dim: 59368 9 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(9): l1 l2 ... w2 w3
colData names(5): cell_type condition sample run runsCollapsed

> colData(ddsColl)
DataFrame with 9 rows and 5 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0)
> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

> dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
> dds
class: DESeqDataSet 
dim: 59368 18 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(18): KO1_P1_L001.Counts KO1_P1_L002.Counts ... WT_P3_L001.Counts WT_P3_L002.Counts
colData names(4): cell_type condition sample run

> ddsColl <- collapseReplicates(dds, dds$sample, dds$run)
> ddsColl
class: DESeqDataSet 
dim: 59368 9 
metadata(1): version
assays(1): counts
rownames(59368): DDX11L1 WASH7P ... MT-TT MT-TP
rowData names(0):
colnames(9): l1 l2 ... w2 w3
colData names(5): cell_type condition sample run runsCollapsed

> colData(ddsColl)
DataFrame with 9 rows and 5 columns
     cell_type condition      sample           run               runsCollapsed
   <character>  <factor> <character>   <character>                 <character>
l1       human   longKO           l1  long_P1_L001   long_P1_L001,long_P1_L002
l2       human   longKO           l2  long_P2_L001   long_P2_L001,long_P2_L002
l3       human   longKO           l3  long_P3_L001   long_P3_L001,long_P3_L002
s1       human   shortKO          s1 short_P1_L001 short_P1_L001,short_P1_L002
s2       human   shortKO          s2 short_P2_L001 short_P2_L001,short_P2_L002
s3       human   shortKO          s3 short_P3_L001 short_P3_L001,short_P3_L002
w1       human   WT               w1    wt_P1_L001       wt_P1_L001,wt_P1_L002
w2       human   WT               w2    wt_P2_L001       wt_P2_L001,wt_P2_L002
w3       human   WT               w3    wt_P3_L001       wt_P3_L001,wt_P3_L002

> matchFirstLevel <- dds$sample == levels(dds$sample)[1]
> matchFirstLevel
logical(0)
> stopifnot(all(rowSums(counts(dds[,matchFirstLevel])) == counts(ddsColl[,1])))
Error: all(rowSums(counts(dds[, matchFirstLevel])) == counts(ddsColl[,  .... is not TRUE

Removed `colnames` command and its output to further reduce the content.

Source Link

edited Jan 13, 2022 at 16:57

Gawain

335
1
10

Loading

Shortened the content as per the request in the comments.

Source Link

edited Jan 13, 2022 at 15:10

Gawain

335
1
10

Loading

deleted 11 characters in body; edited title

Source Link

edited Jan 12, 2022 at 21:49

Gawain

335
1
10

Loading

added 358 characters in body

Source Link

edited Jan 12, 2022 at 19:52

Gawain

335
1
10

Loading

Source Link

asked Jan 12, 2022 at 19:45

Gawain

335
1
10

Loading

Stack Exchange Network

Return to Question