Entering edit mode
Dear Marco,
It is amazing that CASAVA is unable to return read counts. If that is
really true, then perhaps you should switch to a better mapping/count
tool. My lab uses subread, which is better, faster and available as a
Bioconductor package.
You cannot use edgeR (or DESeq) to analyse base counts. The negative
binomial assumptions of those packages would be grossly violated.
However, the limma-voom pipeline for RNA-Seq data would remain valid
for
base counts, and is highly competitive with the negative binomial
approach. limma-voom is optimized for the same sort of quadratic
mean-variance relationship as the negative binomial approach, but
without
making assumptions about the form of the distribution or the absolute
size
of the counts. See the last case study in the limma User's Guide.
Best wishes
Gordon
> Date: Tue, 31 Jan 2012 10:29:19 +0100
> From: Marco Groth <mgroth at="" fli-leibniz.de="">
> To: bioconductor at r-project.org
> Subject: [BioC] BaseCounts & edgeR
>
> Dear Bioconductor team,
>
> I am using DESeq and edgeR for analysis of count data and find
> differentially expressed genes and btw it worked very well. As input
> data I created read count. For that I used also Illumina's CASAVA
and
> GenomeStudio. Unfortunately, Illumia changed the counting procedure.
As
> of version 1.8 read counting is not possible anymore, they changed
> finally to base counting. Means all mappable bases which fulfil a
given
> quality score will be counted. So by using high quality 50bp reads
for
> mapping the counts will be around 50x higher compared to the read
count
> method.
> By using the base counts in edgeR the number of differentially
expressed
> genes is dramatically reduced. We normally compare DESeq and edgeR
> results and they fit around 80%. Using the base counts the results
do
> not fit anymore.
> I divided all base counts by 50 to approximate the read count and
the
> results look better, but not as good as before. Furthermore, I get
> uncertainties because of counting in splice site is more
sophisticated.
> Nevertheless, my question is whether I can run edgeR using base
counts
> and getting good results?
>
> Thanks, Marco
>
> --
>
> Marco Groth
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