[BioC] easyRNASeq read counts varying when recounting same sample!

[René Böttcher]

Dear Nicolas,

I noticed that my read counts are varying when I count the exact same
sample twice. Specifically, genes that have counted reads in the first run
are not represented at all (0 counts) in the second run, while others have
exactly the same counts!

I attached a shortened list of what my count tables look like in a tsv
file, please note that I recounted the samples with the same options and
annotation was provided via biomaRt.
To explain the attached .tsv-file, I recounted the samples in order to make
a comparison of Group1 vs Group1 treated and Group1 vs Group2 using
separate objects.

You can easily see the differences in reads counts in the first sample of
both comparisons (Group1_1412.bam).

Here's how I used the easyRNASeq function:

DGElist = easyRNASeq(organism="Hsapiens",
                annotationMethod="biomaRt",
                gapped=TRUE,
count="genes",
                summarization="geneModels",
                filesDirectory=getwd(),
filenames=bamfiles,
recursive=T,
                normalize=F,
outputFormat="edgeR",
conditions=conditions)

I hope this problem can be solved easily, because I already handed the list
of differentially expressed genes over to a colleague of mine who wants to
validate these genes now.

Best regards,
René