Error in champ.load() function

Question

[Monalisa]

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.

Answer 1

[Basti]

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))
})

[Monalisa]

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?

[Basti]

I tried to download the three samples you provided and it works on my machine. How did you create the pd file ? Maybe there are some files names not matching

[Monalisa]

This is the pd file attached what I have made.

[Monalisa]

[Basti]

Oh yes I see, unfortunately I'm not using excel, it seems it is automatically converting your Slide column to scientific notation

[Monalisa]

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?

[Basti]

It should be a .csv file I just don't use excel because it has drawbacks in bioinformatics