Hello everybody, I have problems in loading files with ChAMP. In particular I hve proble with the pd file (samplesheet), I get back this in R:

[ Section 1: Read PD Files Start ] CSV Directory: C:/Users/utente/methylation_CLL1/Samplesheet_2022-282-ILL_Epic_N=34 (2).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. There is NO Pool_ID in your pd file. There is NO Sample_Plate in your pd file. There is NO Sample_Well in your pd file. Error in champ.import(directory, arraytype = arraytype) : Error Match between pd file and Green Channel IDAT file.

It says that there is no Sentirx_ID and Sentrix_Position, but actually they are present in my csv file (as all the other info requested. And the I do not understand why there is no match between pd file and IDAT file.

Can you help me please?

Thanks,

Giulia

In the code that you used to read in your csv file, you have

pdfile<-read.table(file="C:/Users/utente/methylation_CLL1/Samplesheet_171122 - Copia.csv", sep= ";", header= TRUE)

Whereas ChAMP will use read.csv. If your separators are actually semi-colons (and how else would your code work if not), then ChAMP will end up with a single column data.frame that doesn't have any of the headers that are expected to be there. You could simply do

write.table(pd, file="C:/Users/utente/methylation_CLL1/Samplesheet_171122 - Copia.csv", sep = ",", quote = FALSE, row.names = FALSE)

And then it should work for you.

Also, when you are posting, right below where you type is another box that shows how your post will be formatted. You should spend the time to look at that box and ensure that your post is clear and easy to read, which so far has not been true. Nobody likes trying to read things like

pdfile<-read.table(file="C:/Users/utente/methylation_CLL1/Samplesheet_171122 - Copia.csv", sep= ";", header= TRUE) str(pdfile) list.files("C:/Users/utente/methylation_CLL1")

When in fact it should look like

pdfile<-read.table(file="C:/Users/utente/methylation_CLL1/Samplesheet_171122 - Copia.csv", sep= ";", header= TRUE) 
str(pdfile)
list.files("C:/Users/utente/methylation_CLL1")

Making it easier on people who might want to help you is in your best interest.

This p-value, which I assume indicates the importance of the fold change, should it not be scale-independent? Also, if the threshold is set to 1, shouldn't all of the results be displayed? error in ChAMP loading filebackrooms game

Confirm that the IDAT files are in the correct directory and follow the required naming convention. Make sure the IDAT files are compatible with the specified array type in ChAMP. Consider updating to the latest version of ChAMP and reaching out to the ChAMP community or developers for further assistance.