Questions tagged [deseq2]

Deseq2 is an R package for analyzing RNA sequencing data

10 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
2
votes
0answers
30 views

vst() from DESeq2 vs voom() from limma

I have used both to transform my leukaemia RNA-Seq data for subsequent hierarchical clustering. The result is quite different. Some subtypes of leukaemia only form a cluster (or at least sit closer) ...
1
vote
0answers
234 views

Is it advisable to remove X and Y chromosome genes in a bulk RNA-seq dataset at the level of the count matrix?

From this link remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline, I have learned that depending on context, it is perfectly valid to remove X and Y chromosomal genes in an RNA-seq ...
1
vote
0answers
454 views

Likelihood Ratio Test in DEseq2

I have a RNA seq data which I am trying to identify DEGs. Dataset contains: Untreated - 2 replicates (time point 1st day) Treated - 4 replicates (2 replicates at 3rd day & 2 replicates at 7th ...
0
votes
0answers
18 views

Differential Gene Expression with Replicates for some of the samples

In some specific situations, it is neither affordable nor feasible to have replicates for large RNA-seq analysis. Moreover, the analysis purpose is just hypothesis generation for further experiment ...
0
votes
0answers
23 views

a proper Design Matrix for several drug treatments with both control negative and control positive

I have a dataset of RNA-seq samples for testing different drugs on the presence of another drug. One of my samples is the normal cells with no drugs (control negative) and another is the cells with ...
0
votes
2answers
57 views

RNAseq biological replicates not clustering in PCA plots

I have RNAseq data from 4 samples with 3 biological replicates per sample. I am currently trying to do the differential expression analysis with DESeq2 but the biological replicates will not cluster ...
0
votes
1answer
74 views

DESeqDataSetFromTximport all(lengths > 0) is not TRUE

I am suddenly running into an error when running the DESeqDataSetFromTximport ...
0
votes
1answer
87 views

RNASeq: Normalization, stabilization, gene length and rlog

I was thinking about the best method for normalization, which takes gene length into account (in order to compare genes)... Do you think I can do that? : - taking raw counts and dividing each gene by ...
0
votes
0answers
59 views

Making a model of gene contribution in cancer diagnosis

I have raw read counts (Edgeseq technology) of 56 patients who have been ranked with Mandard score as responders and non-responders; I have done differential expression by DESeq2 and I obtained a ...
-2
votes
1answer
44 views

How can I perform differential expression analysis with DESeq2, starting with a count matrix?

I have a gene expression count matrix with the Gene Symbol IDs as the row headings and the Sample IDs as the column headers. How would I use DESeq-2 for the given data set through R?