This is a test version of Biostars. For the public version, visit https://www.biostars.org.
DESeq2 error :Error in cleanContrast

I'm trying to extract results from DESeq2 anlysis using contrast function, my code is :

zyres_BFvsBS <- results(zinbde_sub, contrast = c("Group.Sub.Group", "BF", " BS"))

But I got this error:

Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, : BF and BS should be levels of Group.Sub.Group such that Group.Sub.Group_BF_vs_A and Group.Sub.Group_.BS_vs_A are contained in 'resultsNames(object)'

I tried this code:

zinbde_sub$Group.Sub.Group <- factor(zinbde_sub$Group.Sub.Group, levels =c("A","BF","BS","CF","CS"))

But it's not working.

Do you have any suggestions? Thank you very much!

deseq2
• 6,699 views • link
updated by jared.andrews07 jared.andrews07 • written by hsu • hsu

Can you post the results of levels(zinbde_sub$Group.Sub.Group)? Also please format your code properly.

• 0 views • link
written by Mark Mark

Please hughlight code/errors with markdown: enter image description here

• 0 views • link
written by ATpoint ATpoint

1 answer

Looks like you have a typo - the error message says the BS is .BS. I'd check your samplesheet or wherever you're defining that group, or try .BS in your results call.

• 0 views • link
written by jared.andrews07 jared.andrews07

Log in to answer this question.

More posts like this