Question: DESeq2 - MAP and MLE - log2FoldChange
0
gravatar for thomasjenner333
17 months ago by
thomasjenner3330 wrote:

Hi, 

I'd used DESeq2 to get a list of differential expressed genes. Initially I had got the following results (showing a few records). The following was done a few months ago.

> res <- results(dds)
> res <- res[order(res$padj),]
> head(res)
log2 fold change (MAP): condition treated vs untreated 
Wald test p-value: condition treated vs untreated 
DataFrame with 6 rows and 6 columns
                    baseMean log2FoldChange     lfcSE      stat        pvalue
                   <numeric>      <numeric> <numeric> <numeric>     <numeric>
gene1  1450.813       6.035077 0.2075759  29.07408 7.637165e-186
gene2  2270.323       4.420449 0.1640810  26.94066 7.340123e-160

                            padj
                       <numeric>
gene1 1.083026e-181
gene2 5.204514e-156

I recently, repeated the analysis using the code on the same count data and I notice that except for the baseMean values the remaining at slightly modified. Showing a few records

> res <- results(dds)
> res <- res[order(res$padj),]

> head(res)

log2 fold change (MLE): condition treated vs untreated 
Wald test p-value: condition treated vs untreated 
DataFrame with 6 rows and 6 columns
                    baseMean log2FoldChange     lfcSE      stat        pvalue
                   <numeric>      <numeric> <numeric> <numeric>     <numeric>
gene1  1450.813       6.307924 0.2237472  28.19219 7.290237e-175
gene2  2270.323       4.536798 0.1688725  26.86523 5.599504e-159

                            padj
                       <numeric>
gene1 1.009042e-170
gene2 3.875137e-155

Can anyone tell me why there is this change. Thank you. 

 

deseq2 • 450 views
ADD COMMENTlink modified 17 months ago by Michael Love24k • written 17 months ago by thomasjenner3330
Answer: DESeq2 - MAP and MLE - log2FoldChange
1
gravatar for Michael Love
17 months ago by
Michael Love24k
United States
Michael Love24k wrote:

You're using a newer version of DESeq2. See the NEWS file for changes. In particular the relevant one was from a year ago, when DESeq() now outputs MLE fold changes. This is described in NEWS and in the vignette.

ADD COMMENTlink written 17 months ago by Michael Love24k

 I'll look into the vignette. Thank you for responding.

ADD REPLYlink written 17 months ago by thomasjenner3330
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