Hi, maybe I am doing something wrong but I cannot find a log2FoldChange inside the results of DESeq2:

res = results(dds, contrast=c("cond", test, control))
dRes = as.data.frame(res)

dRes$log2FoldChange[1]

[1] 12.62795

dRes[dRes$log2FoldChange == 12.62795,]

[1] baseMean       log2FoldChange lfcSE          stat           pvalue        

[6] padj          

<0 rows> (or 0-length row.names)

dRes[dRes$log2FoldChange >= 12.62795,]

                baseMean log2FoldChange     lfcSE    stat        pvalue

                 8602.244       12.62795 0.5325757 23.7111 2.770195e-124

          padj
          3.928413e-120


Same result using directly res without the conversion in data frame.

while:

d = data.frame(a=c(1.2, 1.3), b = c(2.1, 2.2))

d[d$a==1.2,]
    a   b
1 1.2 2.1

Could you please tell if I am filtering the table in the wrong way?

Thank you.

You are looking for a fold change based on a printed value, but R doesn't print all the digits it knows, it prints only 7 digits by default. See here:

https://stat.ethz.ch/R-manual/R-devel/library/base/html/options.html

For example

 > 1/3
 [1] 0.3333333
!> 1/3 == 0.3333333
 [1] FALSE