I was trying to analyse a breast cancer dataset GSE212370. I have made a pd file for that in the prescribed format of ChAMP document which contains column headers as follows (showing only first 3 rows of pd file):
Sample_Name Sample_Plate Sample_Group Pool_ID Project Sample_Well Array Slide Basename Filename
NT1 NA NormalTissue NA NA NA R03C01 201247470004 201247470004_R03C01 201247470004_R03C01
NT2 NA NormalTissue NA NA NA R08C01 200861300050 200861300050_R08C01 200861300050_R08C01
NT3 NA NormalTissue NA NA NA R03C01 200959030050 200959030050_R03C01 200959030050_R03C01
But when I run the following code in R studio,
myload<-champ.load("C://Users//Monalisa//Downloads//GSE212370")
it gave me following error,
[<<<< ChAMP.IMPORT START >>>>>]
-----------------------------
[ Section 1: Read PD Files Start ]
CSV Directory: C://Users//Monalisa//Downloads//GSE212370/GSE212370_pd_edited_new.csv
Find CSV Success
Reading CSV File
Your pd file contains NO Array(Sentrix_Position) information.
Your pd file contains NO Slide(Sentrix_ID) information.
Error in champ.import(directory, arraytype = arraytype) :
Error Match between pd file and Green Channel IDAT file.
Please tell me how to resolve this.
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written
by
Monalisa •
The issue is that the IDAT files are not properly named for champ.load function. Indeed, for instance they contain "_noid" in the filename. So a solution is to rename all the files removing the "_noid" pattern in the file names :
folder = "C://Users//Monalisa//Downloads//GSE212370"
files <- list.files(folder,pattern = "_noid",full.names = T)
sapply(files,FUN=function(eachPath){
file.rename(from=eachPath,to= sub(pattern="_noid", paste0(""),eachPath))
})
Thanks Basti for your reply. I have tried your code and it removed all of the "noid" from my pd file. But the error is same. Is there another reason for the error?
This is the pd file attached what I have made.
as you told you are not using Excel, can you please tell me what is your pd file format? Is it not a csv format?
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