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Gurkenkönig
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@gurkenkonig-16328
Last seen 5.2 years ago
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.
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
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
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.
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.
I am having the same error when I am trying to run the test data follwoing the online documentation.
Is there a solution for this yet?
Best,
R.
Hi:
I just tested, you are right it's not working now. I guess it's because some function/package gets updated, that the ChAMP code needs to be updated.
I will fix it ASAP.
Best Tian
It would be very valuable to add examples or unit tests that exercise this (and other) aspects of the package, so that failures appear in the nightly build report (http://bioconductor.org/checkResults/release/bioc-LATEST/ChAMP/) and can be fixed by the maintainer proactively.
Hi Martin:
Thanks for your suggestion. In past years I am just patching one and another on the package, now I think it's a good idea to start to revise it completely, using some better new packages like datatable, plumber and your suggested unit_test.There are many aspects could be improved compared with 4 years ago.
Best Tian
Hi:
I have fixed the bug, it should be online in 48 hours, also, you can copy from my github to install it now.
Best Tian