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?
In this repository, I provide R code to download bladder cancer data from TCGA (TCGA-BLCA) using the package
TCGABiolinksand then used
DESeq2to analyze the data. If you want to give it a try, just replace "TCGA-BLCA" with your cancer of interest TCGA abbreviation.
Hamid Ghaedi , the
repositoryyou provided has really been helpful. however, I have problem with this syntax
write.csv(res_df, file= paste0(resultsNames(dds), ".csv")initially I corrected it by adding a close bracket. But then, after running the code, I got this as saved file
I ran this before the
result_df <- as.data.frame(res_output)
result_df$ensembl_gene_id <- row.names(result_df)
result_df <- merge(df,result_df, by = "ensembl_gene_id") resOrdered<-result_df[with(result_df, order(abs(log2FoldChange), padj, decreasing = TRUE)), ]
I have tried all I can but it seems am not getting solution. is there something am doing wrong?
Jakpa Thanks for mentioning the closing bracket :). Can you change the values you have passed to
alpha=(let's set this as 0.1) and/or
lfcThreshold =(let's set this as 0.5) in the following chunk in your code? Then run the code and inspect the result
Hamid Ghaedi , Thank you for your response. But, its still same output. i.e, empty rows
I couldnt figure the reason:)
Then open a new question and provide all the code you are using, and you will get feedback.
Leo, do not delete posts that have received feedback.