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7 votes
Accepted

How is prior.count used by edgeR's cpm

The prior count ends up getting scaled by the ratio of a library size to the average library size and then multiplied by 2 before getting added to each library size (I'm sure there's a good reason for ...
Devon Ryan's user avatar
  • 19.7k
6 votes
Accepted

When performing differential expression analysis, should genes with low read counts be removed before or after normalization?

The more genes you have the more robust the scaling factor is (among the reason why one doesn't normalize to ERCC spike-ins without a compelling reason), so I suppose in theory it's better to filter ...
Devon Ryan's user avatar
  • 19.7k
5 votes

Why use "robust" FPKMs?

FPKM are inherently experiment specific and can not be used to compare across samples. Let's consider the following two sequencing runs. Let $E1$ and $E2$ be the true, underlying expression in two ...
Bastian Schiffthaler's user avatar
5 votes
Accepted

What do these files / annotations mean?

You are looking at the supplementary data of a paper. That seems to have given you a list of features, and some information about those features. Specifically, you seem to have a list of two types of ...
terdon's user avatar
  • 10.2k
4 votes

Error in quantile.default(x, p = p) in EgdeR calcNormFactors

Ok, it turned out that some rows and/or columns contained all values as zeros and that was the reason for the error. I wrote a function to fix that: ...
Nikita Vlasenko's user avatar
4 votes

Identify differentially covered genes only between two samples

Not really an answer but an extended comment... and most likely something you don't like to hear I guess by technical replicates, it means taking the same biological sample and making 2 methylation ...
StupidWolf's user avatar
  • 1,688
4 votes
Accepted

How to incorportate RIN values as covariate in the design matrix?

In the DESeq2 manual there is a section titled "How can I include a continuous covariate in the design formula?" that deals with your question. Basically the process is no different from using a ...
PPK's user avatar
  • 886
4 votes
Accepted

DESeq2 for large number of samples takes too much RAM

I'll preface this by saying that I don't think DESeq2 is the right tool to use for ATAC-Seq data. My own study of ATAC-Seq patterns [admittedly only a couple of runs that were our first exploration of ...
gringer's user avatar
  • 14.4k
3 votes

Basic RNA Differential Expression in R

See here for a Differential Expression guide which discusses carrying out differential expression using DESeq2: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html ...
gringer's user avatar
  • 14.4k
3 votes

Experimental Design for Differential expreression analysis

You're really running out of degrees of freedom and the only actual replicate is a single sample from another patient, so please take the results with a huge grain of salt. You can use a design of <...
Devon Ryan's user avatar
  • 19.7k
3 votes

*very* unbalanced group sizes for DE

In general, you would expect roughly the same distribution on both sides of your volcano plot. The first two plots are concerning since there's so much on the right and not on the left. With such a ...
pstew's user avatar
  • 131
3 votes

*very* unbalanced group sizes for DE

Random partitioning (as you have done) seems like a reasonable thing to do to work out what's going on. From the results you have suggested, it looks like DESeq2 is performing better than EdgeR, so ...
gringer's user avatar
  • 14.4k
3 votes

Batch Effects in RNA Seq Sample

The help page for removeBatchEffect() explicitly states that it should not be used in conjunction with differential expression testing, so don't do that. You ...
Devon Ryan's user avatar
  • 19.7k
3 votes

How to calculate logCPM across all samples?

If you want the values by group then subset y to contain the samples of interest and then feed that to aveLogCPM().
Devon Ryan's user avatar
  • 19.7k
3 votes
Accepted

DE analysis tool and method for non-coding features

The post here is useful ... https://support.bioconductor.org/p/76790/ ExactTest is really cool and completely different from ...
M__'s user avatar
  • 12.6k
2 votes

What could be the reason for the samples not clustering?

Samples will only cluster by experimental group if the experimental effect is large enough that it's the primary source of variance between your samples. If that's not the case then you'll get results ...
Devon Ryan's user avatar
  • 19.7k
2 votes

confidence ellipses for MDS plot in edgeR?

I can see that there would be a three step process to doing this: Merge counts from all samples in the group and then resample pseudo-replicates from this. If x is ...
Ian Sudbery's user avatar
  • 3,321
2 votes
Accepted

RNA-seq: How to get new expression count after normalization

If I'm interested to get normalized gene counts, can I go ahead and multiple each individual's norm.factor into its gene counts? For example, the expected count for IND1 for Gene1 is 100 and it's ...
swbarnes2's user avatar
  • 1,941
2 votes

Identify differentially covered genes only between two samples

You may run edgeR for methylation analysis without replicates (https://f1000research.com/articles/6-2055). But I also recommend you to have a look at the R DSS package. It has a smoothing step which ...
thomas duge de bernonville's user avatar
2 votes
Accepted

What is the difference between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus for converting to gene symbols?

AnnotationDBi uses AnnotationDb objects which is the virtual base class for all annotation packages. It contain a database ...
Nitesh Shriwash's user avatar
2 votes
Accepted

plotting gene expression after EdgeR DE analysis using RUVg (RUVseq) covariates

You could correct your logCPMs (edgeR::cpm(y, log=TRUE)) with the covariates from RUVseq using limma and then use these for plotting: ...
alderaan_shot_first's user avatar
2 votes
Accepted

DESeq2 and EdgeR

I think your question has been answered very well here: https://www.biostars.org/p/284775/ If you want to go deeper perhaps you can look at this paper by Li et al. https://genomebiology.biomedcentral....
Avamys's user avatar
  • 118
2 votes

Batch correction in differential expression analysis

If both batches contain replicates of both groups (LT and C) then the presented code is what you should do, exactly pointed out in the vignette for the LRT: http://bioconductor.org/packages/release/...
ATpoint's user avatar
  • 1,430
1 vote

Basic RNA Differential Expression in R

I'm thinking first normalize using TMM then compare the mean of the normalized values for treated vs. untreated? That is a bit too simple. You need to analyse your experiment as a paired comparison. ...
Gordon Smyth's user avatar
1 vote

the variation between treatments is less than the variation between replicates in RNA-seq data

If you got DEGs with statistically significant p-values after multiple testing following a valid pipeline, I'd believe that, even if looking at the first few PCs doesn't look promising.
swbarnes2's user avatar
  • 1,941
1 vote

RNASeq analysis using featureCount and EdgeR

It makes no difference if you process the BAM files one at a time with featureCounts or all together, except that it changes how you have to read the files into R. You can supply edgeR with lists of ...
Devon Ryan's user avatar
  • 19.7k
1 vote

Determining what RNAseq data is filtered on volcano plot

edgeR functions do not do any filtering, i.e., they do not remove any genes from the results or from the plots. The only filtering was that which you did explicitly yourself by: ...
Gordon Smyth's user avatar
1 vote

Bulk RNA-Seq Read Length Normalization across different samples

The simplest thing to do is to trim the 150 bp fasts so that they are 100 long. I don't think there is an easy way to correct for the fact that the 150 bp long reads will have a higher unambiguous ...
swbarnes2's user avatar
  • 1,941

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