Question: champ.runCombat is failing: "invalid 'row.names' length"
gravatar for Gurkenkönig
11 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 • 547 views
ADD COMMENTlink written 11 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 11 months ago by Yuan Tian110

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 11 months ago by Yuan Tian110
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