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Question: problem with the dba() function in DiffBind
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gravatar for mm2489
2.8 years ago by
mm24890
United States
mm24890 wrote:

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.

ADD COMMENTlink modified 2.8 years ago by Rory Stark2.4k • written 2.8 years ago by mm24890
0
gravatar for Rory Stark
2.8 years ago by
Rory Stark2.4k
CRUK, Cambridge, UK
Rory Stark2.4k wrote:

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

ADD COMMENTlink written 2.8 years ago by Rory Stark2.4k

Thanks Rory

I emailed the files to you.

I appreciate your help

ADD REPLYlink written 2.8 years ago by mm24890
0
gravatar for Rory Stark
2.8 years ago by
Rory Stark2.4k
CRUK, Cambridge, UK
Rory Stark2.4k wrote:

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

ADD COMMENTlink written 2.8 years ago by Rory Stark2.4k

Thanks Rory

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

ADD REPLYlink written 2.8 years ago by mm24890

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

ADD REPLYlink written 2.8 years ago by Gord Brown570
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