question about DiffBind

Question

[mikysyc2016]

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!

Answer 1

[Federico Giorgi]

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

[mikysyc2016]

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!

[Rory Stark]

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.