Hi, there.
I noticed that the DESeq2 package (Version 1.20.0) has some changes comparing to the previous versions.
When extracting the results, I firstly got res <- results(dds, alpha = 0.05, lfcThreshold = 1) to obtain the set of results, it only got 8 significant microbiome taxa, and 4 LFC >1, 4 LFC < -1 according to the summary( ) function of the results.
However, if I set up the lfcThreshold = 0 in the results function, such as res <- results(dds, alpha = 0.05, lfcThreshold = 0), then filter the log2fold change by using the information in the res table as following:
res.positive <- res[res$log2FoldChange > 1 & res$padj < 0.05 & !is.na(res$padj),]
I actually get way more than just 4 results, which is inconsistent with the results filtered using lfcThreshold = 1
I am just wondering whether I misunderstood the lfcThreshold argument and the log2FoldChange in the result table are the same thing, but they are actually not?
I also tried to rerun some of my old codes (generated using an older version of the DESeq2 package in another laptop), there was no such discrepancy, then I updated the package in the other laptop, I couldn't replicate my old results.
Really need some clarification here.
Thank you so much!
Yan
