This is a test version of Biostars. For the public version, visit https://www.biostars.org.
question about DiffBind

Hi all,

I get the error from R, when I try to use DiffBind. Do not understand what is this?

tamoxifen <- dba(sampleSheet="tamoxifen.csv", dir(path = system.file("extra", package="DiffBind")))

Error in dba(sampleSheet = "tamoxifen.csv", dir(path = system.file("extra",  : 
  DBA object is a character string; perhaps meant to be argument 'sampleSheet'?

Thanks!

chip-seq r
• 3,450 views • link
updated by zx8754 zx8754 • written by mikysyc2016 mikysyc2016

1 answer

Hi there,

I believe you are using a not up-to-date example. In DiffBind 2.4.0+ you achieve what you want to do (i.e. loading the example sample sheet) like this:

library(DiffBind)
setwd(system.file("extra", package="DiffBind"))
tamoxifen <- dba(sampleSheet="tamoxifen.csv")

Check ?dba for all details

• 1 views • link
written by Federico Giorgi Federico Giorgi

Hi, I use your suggestion, it works for tamoxifen samples ( which is an example of DiffBind). When i do my data analysis, i met another problem. Do you know how to deal with it?

setwd(system.file("extra_1", package="DiffBind")) ppara <- dba(sampleSheet="ppara.csv") 1 FAT ppara wt 1 bed Error in if file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed

Thanks!

• 1 views • link
written by mikysyc2016 mikysyc2016

This is telling DiffBind to look in a specific directory within the package installation for the samplesheet file. This is very non-standard -- it only looks there for the example samplesheet as this is part of the installation itself. The specific error is that the first peak file doe not exist where you are specifying it. If you are specifying the peak files in a relative location, they may not be found as you have changed the working directory to the installed library.

• 1 views • link
written by Rory Stark Rory Stark

Log in to answer this question.

More posts like this