Question: champ.runCombat is failing: "invalid 'row.names' length"
gravatar for Gurkenkönig
9 months ago by
Gurkenkönig0 wrote:

I have read in an existing matrix of 450K beta values with champ.filter and linked it to a dataframe of covariates. So far everything worked perfectly (champ.QC, champ.norm, champ.SVD) only in champ.runCombat I always get the same error message.

<< Preparing files for ComBat >>
[Combat correction will be proceed with 414206 probes and 373 samples.]

Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

Can anyone give me a hint what could be the problem? When checking the covariates and the beta matrix I can't see any problems at the first glance.

champ • 441 views
ADD COMMENTlink written 9 months ago by Gurkenkönig0


Could you show send your pd file (Sample_Sheet.csv) to me to check what's wrong with it? To email


Yuan Tian

ADD REPLYlink written 9 months ago by Yuan Tian90

By the way, could you please check if the batch varaible (say Slides) in your pd is "Character" or "Factor" format? I found that some users' "Slides" column is numeric, which might triggle this error.

To check the format, use code: class(pd[,X]).

If it's numeric, to change the format, use code: pd[,X] = as.character(pd[,X])

Then you may retry the code.


Yuan Tian

ADD REPLYlink written 9 months ago by Yuan Tian90
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