Hello,

 I performed DESeq2 to analyze DE genes between two groups (control vs
treatment) using 30 samples in each group. I got more than 790 (the
result is attached) DE genes using FDR 10%. However, the values of
log2folchange were lower than 1 (the MA plot is attached). Now I started
to write my paper and I saw that several authors used log2foldchange > 1
as cutoff to downstream analysis as functional analysis. Do you think
that I can't proceed my functional analysis? Thanks.

Sometimes a fold change cutoff is/was used by some authors in lieu of a proper statistical model. If you care about any amount of differential expression (any log fold change greater than 0 in absolute value) you can use the FDR cutoff. DESeq2 is sensitive to small, true differences as well as large true differences, all while controlling specificity/false positives. If however you only care for biological reasons about large log fold changes (larger in absolute value than some positive value), use the 'lfcThreshold' argument to results. See ?results for more information and the threshold section of the vignette.