Hello, I am sorry for this newbie question, but I spent all morning trying to find it out but can't find a clear answer anywhere.
I want to normalise RNA seq data from TCGA using DESeq2. I use the TCGA-Assembler R package to download RNA seq data using array platform: "gene_RNAseq" which gives an excel with raw_count and scaled_estimate for each patient sample and gene. Should I use the "ProcessRNASeqData" function from the TCGA-Assembler package or just go with the excel file given by the "DownloadRNASeqData" function?
Then before I can start using DESeq2, I have to create a count matrix. How do I do this? Does anyone perhaps have any code ready that I can use for this type of data?
I really would appreciate any help because I have no idea how to continue. Thanks!
edit: read somewhere that I should download "illuminahiseq_rnaseqv2-RSEM_genes_normalized (MD5)" from firehose. how can I convert this data so I can use it for DESeq2?