Hope you all doing well 🙂

I have a question regarding extracting differentially expressed genes identified with the global method of the `decideTests` function from limma. I have 7 contrasts that are related to each other. From the user guide, it is advised to adjust for BETWEEN cotnrasts as well in cases like mine using `method="global"`. I found an answer in other posts that the results from `decideTests` can be extracted using the `` function from limma as follows :, adjust="BH", method="global", file="globalDEresults.txt")

However, I have 2 questions about this method:

**1)** Using `` function outputs a large file for **ALL** contrasts with their log fold change, p values, t statistcs and adjusted p-values in **ONE** file. This requires more work to make it tidy per contrast. Normally speaking(if `method=separate`), `topTable` function would allow me to extract results per contrast by changing the coef option as follows:

dpe_ckd_alone<-topTable(fit3, coef="CKD_alonevsNoCOM",number = nrow(fit3))

***So, my question is:*** is there a similar method to toptable when you are correcting for between contrasts using `method=global` from `decidetests`? Otherwise, how would you extract results per contrasts easily and assign them to an object?

**2)** If I don't want to extract the results directly to excel or txt file, but would rather want to manipulate it in R before exporting it, Is it possible to assign the dat ...

Source link