[BioC] Estimating Size Factors in DESeq Package

Simon Anders anders at embl.de
Fri Sep 7 23:20:30 CEST 2012

Dear Andres

On 09/07/2012 05:05 PM, Andres Eduardo Rodriguez Cubillos wrote:
> Overall, I organized my tables quite similar to the
> pasilla_gene_counts.tsv file you used in your guide "Analyzing
> RNA-seq Data with the DESeq Package" from 2012. At first I had two
> tables: one per replicate containing FPKMs for the three conditions
> analyzed. I then merged the FPKMs of both files to obtain three

FPKM values are not suitable as input data for DESeq. Please see the 
vignette, which states, in Section 1:

The count values must be raw counts of sequencing reads. This is
important for DESeq's statistical model to hold, as only raw reads allow
to assess the measurement precision correctly. (Hence, do not supply
rounded values of normalized counts, or counts of covered base pairs.)


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