Unable to create pd file for ChAMP analysis

Unable to create pd file for ChAMP analysis

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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,

  1. How do I get the “Array” and “Sample_Well” information for TCGA BRCA Methylation Data?
  2. Are these txt files of TCGA BRCA methylation are already normalized?
  3. Should I use “idat files” instead of txt files as input files to be used in ChAMP?
  4. 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.


ChAMP

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