problem with the dba() function in DiffBind
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mm2489 • 0
@mm2489-7705
Last seen 4.2 years ago
United States

I'm trying to use DiffBind for re-analyses of some data. The only files that are changed from my previous run of DiffBind are the peak files from MACS2. They are still in the same format as before. Previously I was able to run Diffbind and analyse this same dataset without errors. However, now when I try the very first step of DiffBind (ta <- dba(sampleSheet="

metadataBROAD.csv"), I get the following message:

> ta <- dba(sampleSheet="metadataBROAD.csv")

0-2k4   pMet  1 macs
Error in `[.data.frame`(peaks, , 2) : undefined columns selected
In addition: Warning messages:
1: In read.table(samplesheet, sep = ",", stringsAsFactors = F, header = T) :
  incomplete final line found by readTableHeader on 'metadataBROAD.csv'
2: In read.table(fn, blank.lines.skip = T, header = T) :
  line 1 appears to contain embedded nulls
3: In read.table(fn, blank.lines.skip = T, header = T) :
  line 2 appears to contain embedded nulls
4: In read.table(fn, blank.lines.skip = T, header = T) :
  line 3 appears to contain embedded nulls
5: In read.table(fn, blank.lines.skip = T, header = T) :
  line 4 appears to contain embedded nulls
6: In read.table(fn, blank.lines.skip = T, header = T) :
  line 5 appears to contain embedded nulls
7: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  embedded nul(s) found in input

 

I can't figure out what the problem is.
Any help would be greatly appreciated.

diffbind • 1.9k views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 14 days ago
CRUK, Cambridge, UK

Hi Mahya-

If you could send me your samplesheet (metadataBROAD.csv) and at least the first MACS2 peak file (0-2k4), I can troubleshoot this.

Also, what version of DiffBind are you using?

Cheers-

Rory

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Thanks Rory

I emailed the files to you.

I appreciate your help

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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 14 days ago
CRUK, Cambridge, UK

Hi Mahya-

I've had a look and see the issue but I'm not sure exactly how the MACS2 peak files were generated.

The problem is that, while MACS2 uses the .xls extensions for the peak files, they are actually tab-delimited ASCII files. The peak file you sent me is a binary Excel file. The sample sheet actually refers to as an .xlslx file (which is not supported), although the file you sent is .xls.

Did the peak file you sent come directly from MACS2, or was it re-saved as an Excel .xls file separately?

-Rory

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Thanks Rory

The peak files were re-saved as .xls separately. How can I fix this issue?

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Hi,

It should be sufficient if you open them in Excel, then save them as "tab-delimited text".  Or try to get the original files, if they are hidden away somewhere.

Cheers,

 - Gord

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