[Bioc-devel] R: Re: Deseq2 and differentia expression

[jarod_v6 at libero.it]

Dear Professo 
Thanks for the clarification. 
I'd like to use that method as a starting list for do some enrichment analisys 
using SPIA.
res <-results(dds)
ddsNoPrior <- DESeq(ddHTSeq, betaPrior=FALSE) #only for lessABs
resGA <- results(ddsNoPrior, lfcThreshold=.5, altHypothesis="lessAbs") 
#greater tdi 
resGA2 <- results(dds, lfcThreshold=1, altHypothesis="greaterAbs") #greater 
tdi 
If I try to see  what change in logfoldchange in this methods I have this 
results:
table(resGA2$log2FoldChange == res$log2FoldChange )

 TRUE 
54927 
ie.
resGA2$log2FoldChange[1]
[1] 0.2104923
> res$log2FoldChange[1]
[1] 0.2104923


So What is wrong? I'm interest to have a list of genes are greater than 1 and 
use as de.genes for the spia package. Here don't found difference!!
thanks in advance for kind help and patience!
jarod

>----Messaggio originale----
>Da: anders at embl.de
>Data: 12/07/2014 10.41
>A: "Bioconductor List"<bioconductor at r-project.org>
>Cc: <jarod_v6 at libero.it>
>Ogg: Re:  Deseq2 and differentia expression
>
>[Reposting from bioc-devel to bioconductor, where this mail should have 
freater than 1 and use as de.genes for the spia package. Here don't found 
difference.

>gone to]
>
>Hi Jarod
>
>Mike overlooked one point in your question
>
>On 11/07/14 12:05, jarod_v6 at libero.it wrote:
>> If I interested in the genes that have a foldchange more than 0.5 and 2 I 
need
>> to use this comand is it right?
>
>DESeq2 reports al fold changes on a log2 scale. So your limits of 0.5 
>and 2 for unlogarithmized fold changes translate to -1 and +1 on the 
>log2 scale (because 2^(-1)=0.5 and 2^1 = 1, with '^' meaning 'to the 
>power of').
>
>Also, the 'lfcThreshold' parameter wants an _absolute_ log fold change. 
>Hence, you want:
>
>ddsNoPrior <- DESeq(ddHTSeq, betaPrior=FALSE)
>res <- results(ddsNoPrior, lfcThreshold=1, altHypothesis="greaterAbs")
>
>to get a list of all genes with an absolute log2 fold change greater 
>than 1, i.e., all genes with a log2 fold change greater than 1 or less 
>than -1, i.e., all genes with fold change below 0.5 or above 2.
>
>Then, in the results table, look at the log2FoldChange column to see 
>which genes went up and which went down.
>
>   Simon
>