Closed farzaneafzali closed 1 year ago
Solved:
My data was insanely huge and consisted multi-layers of lists in the DEXSeqResults that I wasn't able to either convert to data.frame nor doing anything on it. At last, I saved the results of analysis in a .RData Image by:
save.image(file='file.RData')
And then opened it in a GUI Rstudio to study what's going on. My tries there to convert subsets of this result to data.frame was also not successful. At the end, I took a subset of my results less tha pvalue 0.05 and then did write.table from that.
dxr1.sig <- as.data.frame(dxr1[dxr1$pvalue < 0.05 & !is.na(dxr1$pvalue),])
write.table(dxr1.sig, "AS_differential.txt", sep="\t", quote=F)
Hi, I tried several ways to get the result of Rscript step but it doesn't write the table for me. This is the error I get:
I think it might be due to having a list but my tries for flattening the list (which I don't know which column might be) didn't work. I tried this flattening code: df <- apply(df,2,as.character) and then tried to write.csv but no luck, either.
Before that error there is a warning as well:
I should also mention that I get one text file (AS_differential.txt) but it just has one row!
Can someone help to solve this issue please? Thanks a lot. :)