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Question: How to export rld (rlog) or vsd values from DESeq2?
0
gravatar for LuisNagano
9 months ago by
LuisNagano • 10
University of Campinas
LuisNagano • 10 wrote:

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!
rna-seq deseq2 vsd rlog • 855 views
ADD COMMENT • link •
modified 9 months ago by WouterDeCoster ♦ 41k • written 9 months ago by LuisNagano • 10
0
gravatar for WouterDeCoster
9 months ago by
WouterDeCoster ♦ 41k
Belgium
WouterDeCoster ♦ 41k wrote:

Googling rld DESeq2 already gives me the answer, e.g. here
ADD COMMENT • link written 9 months ago by WouterDeCoster ♦ 41k

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.

ADD REPLY • link written 9 months ago by LuisNagano • 10

And what about something like

rld <- rlog(dds, blind=FALSE)
write.csv(rld, file="rld.csv")
ADD REPLY • link written 9 months ago by WouterDeCoster ♦ 41k

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
ADD REPLY • link written 9 months ago by LuisNagano • 10
0
gravatar for WouterDeCoster
9 months ago by
WouterDeCoster ♦ 41k
Belgium
WouterDeCoster ♦ 41k wrote:

Right, what about

rld <- assay(rlog(dds, blind=FALSE))
ADD COMMENT • link written 9 months ago by WouterDeCoster ♦ 41k

Worked it out! Thank you, WouterDeCoster

ADD REPLY • link written 9 months ago by LuisNagano • 10
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