Hi guys, i want to export the rlog values from DESeq2 or vsd, but i only got the dds counts, using the following script:
countsdds <- counts(dds, normalized = TRUE)
write.csv(countsdds, file="dds_norm_counts.csv")
Is there a way to export rlog values?
Thanks for your help!
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LuisNagano •
Googling rld DESeq2 already gives me the answer, e.g. here
Thank you, WouterDeCoster, but i don't want to apply the functions "rlog" or "vst", I just did that. I want to export the output values after run the function, like .csv or .xlsx format table to my directory.
And what about something like
rld <- rlog(dds, blind=FALSE)
write.csv(rld, file="rld.csv")
I tried, but happens that error:
rld <- rlog(dds, blind=FALSE)
write.csv(rld, file="rld.csv")
Error in as.vector(x) : no method for coercing this S4 class to a vector
Right, what about
rld <- assay(rlog(dds, blind=FALSE))
Worked it out! Thank you, WouterDeCoster
Thank you! I was trying to extract my variance stabilizing transformation and write it to a .csv. Got it to work with this:
vst_write <- assay(vst(dds, blind=FALSE))
write.csv(as.data.frame(vst_write), file="VST_results.csv")
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