Question: champ.runCombat is failing: "invalid 'row.names' length"
0
gravatar for Gurkenkönig
15 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.

[===========================]
[<< CHAMP.RUNCOMBAT START >>]
-----------------------------
<< 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 • 787 views
ADD COMMENTlink written 15 months ago by Gurkenkönig0

Hello:

Could you show send your pd file (Sample_Sheet.csv) to me to check what's wrong with it? To email champ450K@gmail.com.

Best

Yuan Tian

ADD REPLYlink written 15 months ago by Yuan Tian120

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.

Best

Yuan Tian

ADD REPLYlink written 15 months ago by Yuan Tian120

I am also getting the same error message and my Slide column is in character format already.

Any ideas what else may cause this error message?

There are 16 samples in my pd and in myNorm. Everything appears to be correct.

ADD REPLYlink written 9 weeks ago by h.curley0

I am also getting the same error message and my Slide column is in character format already.

Any ideas what else may cause this error message?

There are 16 samples in my pd and in myNorm. Everything appears to be correct.

ADD REPLYlink written 9 weeks ago by h.curley0
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