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 7.4 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 • 5.9k views

ADD COMMENT • link updated 7.4 years ago by Michael Love 41k • written 7.4 years ago by becca.grant149 • 0

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change the intgroup to this

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

ADD REPLY • link 4.9 years ago chaimolwangjing • 0

score 0 · Answer 1 · 2016-11-26

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Michael Love 41k

@mikelove

Last seen 4 hours 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 7.4 years ago Michael Love 41k