Error in ChIPQC
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Entering edit mode
lindahove ▴ 10
@lindahove-8760
Last seen 6.3 years ago
Denmark

 

Hi,

I have made a sample sheet on 49 samples containing both histone marks, pol2 and transcription factors (TF).

Its sample sheet I was able to read with ChIPQC() function without any errors. As I was recommended to handle broad marks  separately I split the data sheet. However now I get the following error on the TF sample sheet  when trying to run ChIPQC:

Error: 1 errors; first error:

  Error in colMeans(CoverageMatrix): 'x' must be an array of at least two dimensions

For more information, use bplasterror(). To resume calculation, re-call

  the function and set the argument 'BPRESUME' to TRUE or wrap the

  previous call in bpresume().

First traceback:

  31: ChIPQC(data, annotation = "mm10", chromosome = NULL, blacklist = "mm10-blacklist.bed")

  30: bplapply(samplelist, doChIPQCsample, experiment, chromosomes,

          annotation, mapQCth, blacklist, profileWin, fragmentLength,

          shifts)

  29: bplapply(samplelist, doChIPQCsample, experiment, chromosomes,

          annotation, mapQCth, blacklist, profileWin, fragmentLength,

          shifts)

  28: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM)

  27: bplapply(X, FUN, ..., BPRESUME = BPRESUME, BPPARAM = BPPARAM)

  26: mclapply(X = X, FUN = FUN, ..., mc.set.seed = BPPARAM$setSeed,

          mc.silent = !BPPARAM$verbose, mc.cores = bpworkers(BPPARAM),

 

What does this mean ? 

Cheers Linda

chipseq ChIPQ • 969 views
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Entering edit mode

hi Linda, 

Could you send me a copy of the samplesheet which worked and the new one that didnt?

 

thanks,

 

tom 

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Entering edit mode

hi Linda, 

Could you send me a copy of the samplesheet which worked and the new one that didnt?

 

thanks,

 

tom 

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Entering edit mode
@valerie-obenchain-4275
Last seen 2.1 years ago
United States

Hi Linda,

I'm not that familiar with ChIPQC() but I think the first error message is the important one:

  Error in colMeans(CoverageMatrix): 'x' must be an array of at least two dimensions

The CoverageMatrix (aka 'x') must have 2 dimensions. The ?ChIPQC man page says the 'experiment' argument must be a data.frame or file name. After you split you datasheet are you still passing a data.frame as 'experiment'?

Valerie

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