Question: Ascend runDESeq() not finding factors
gravatar for cf556
9 months ago by
cf55610 wrote:

Hello, I am not sure if this is the best place to post this, but I figured here I have the best chance of getting an answer, currently I am trying to run ascend's runDESeq() function and am getting the following error.

runDESeq(em.set, group = "cluster", parallel = FALSE, method = "pooled-CR")

Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels

Now as far as I can tell I should have at least two levels as there are three clusters, I am not sure what I am doing wrong. Any advice is appreciated.

rna-seq ascend deseq • 192 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 9 months ago by cf55610

Is cluster a factor or just a character class vector?

ADD REPLYlink written 9 months ago by RamRS27k
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