Dear All,
I am trying to understand what does one tailed p-values calculated in a DESeq2 analysis by setting the lfcThreshold to 0 and specifying the alternative hypothesis (as specified here: post) mean in biological terms. In a standard DESeq2 analysis we test for whether a gene is differentially expressed (DE) or not and a two-sided testing is done. Does the one-sided testing mean that we test whether a gene is DE and is up-regulated or DE and is down-regulated depending on the specification of the alternative hypothesis? Is my understanding correct or am I missing something here?
Also, in case I have multiple RNA-seq studies and I want to do a meta-analysis, can the one-sided p-value obtained from DESeq2 for a gene in each of the studies be used for combination of p-values using the Fisher or Stouffer's method? As is the case in microarray data where one can use one-sided p-values from individual studies for a gene. Or do I need to discard the genes with inconsistent expression direction across studies in case of RNA-seq meta-analysis for DE?
Thank you.
