Question

how to fix this error: the argument 'intgroup' should specify columns of colData(dds)

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becca.grant149 • 0

@beccagrant149-11921

Last seen 8.3 years ago

how do I fix this error message?

> plotPCA(rld,intgroup=c("condition","type"))
Error in .local(object, ...) :
the argument 'intgroup' should specify columns of colData(dds)

deseq2 • 6.8k views

ADD COMMENT • link updated 8.3 years ago by Michael Love 43k • written 8.3 years ago by becca.grant149 • 0

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change the intgroup to this

plotPCA(rld,intgroup=c("condition","sizeFactor"))

ADD REPLY • link 5.9 years ago chaimolwangjing • 0

score 0 · Answer 1 · 2016-11-26

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Michael Love 43k

@mikelove

Last seen 9 days ago

United States

Simply reading the content of the message printed here, the function is expecting condition and type to be the names of columns of:

colData(dds)

Is this the case?

ADD COMMENT • link 8.3 years ago Michael Love 43k