Problems In Creating Diffbind Object In R For Chip-Seq Peaks

Question

[Diana]

Hi everyone,

Previously I asked a question here about finding overlapping and unique peaks between two TFs from chip-seq experiments and I got really good answers for that. I have been trying to test one of the methods to achieve this task as was suggested. This method which can be used in R is DiffBind. The problem that I am facing with this is that I just cannot create the object to apply any of the functions from this package. I have peak files in bed format for the two TFs that look like this:

chr1    79092406    79094792    chr1-559    442.2    +
chr1    198383685    198385392    chr1-2813    439.5    +
chr1    200988993    200993982    chr1-141    400.5    +
chr1    63836348    63842294    chr1-24549    296.8    +

and here's the DiffBind manual:

http://www.bioconductor.org/packages/2.11/bioc/manuals/DiffBind/man/DiffBind.pdf

This is how im trying to create the object. I've converted my files to csv and then applied this:

TF1_dba = dba(sampleSheet="TF1.csv")

but it keeps giving me this error:

1     NA raw
Error in file(file, "rt") : invalid 'description' argument

Can anyone tell me what I'm doing wrong?

Thanks a lot!!!

Answer 1

[crysis405]

I have been getting this error when I created the sample sheet in LibreOffice. I traced the problem down to my .csv file being tab delimited instead of comma delimited and managed to get it working. This page might help if you are using libreoffice: Importing and Exporting CSV Files

Let me know if this helped.

[Diana]

Thanks a lot for your answer. However I am using excel and not LibreOffice and I haven't had this problem with any of my other csv files so I'm not sure how I can fix this.