I have downloaded TCGA-BRCA DNA methylation (of data type: Methylation Beta Value) of 895 samples (txt files, not idat files) from GDC portal. That csv file contains CpG probe Ids as rownames and TCGA Ids as column names. I wanted to analyse it through ChAMP. For that I tried to load it on ChAMP using champ.load() function. But the file needs a supporting phenoData or pd File to upload along with beta value file. There is a format of pd in the ChAMP documentation which suggests a file with column headers such as "Sample_Name", "Sample_Plate", "Sample_Group", "Pool_ID", "Project", "Sample_Well", "Array", "Slide", "Basename", "Filenames". I have all the informations from downloaded samplesheet from TCGA_GDC portal, except "Array" or "Sample_Well" information. So I couldn't create the pd file.
My queries are,
- How do I get the "Array" and "Sample_Well" information for TCGA BRCA Methylation Data?
- Are these txt files of TCGA BRCA methylation are already normalized?
- Should I use "idat files" instead of txt files as input files to be used in ChAMP?
- Is there "Array" and "Sample _Well" information available for idat files in TCGA GDC portal? If not how pd files are made for idat files for analysis on ChAMP?
Please help me in this and give your suggestions.
Hi! I hope you solved your problem. I think you could make those two columns with the headers and keep them empty as you don't have the information. After all we only need sample name and sample group- these two columns. I was wondering whether u could give me an answer. I have one excel file containing all probe IDs and beta values for all samples. When I am trying to load it using champ import I am getting error message that no correct match between pd and green idat file. I created a pd file (.CSV file) alright in the same folder with sentrax id etc. But I am not understanding how to convert the excel into a matrix or what should be my command instead of champ.import. Could you please help me? Thanks a lot