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. 

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.