TCGA data - TCGAbiolinks

Question

[fadimeoztoprak]

I want to know the difference between TCGA data we download from firebrowse.org and TCGA data we download with GDCdownload function. The things i realized;

• Categorization is different between two. At firebrowse we can download results of mRNASeq for example. With GDCdownload we can get "Gene expression quantification, isoform expression.." so on.
• Firebrowse data has 1 more column and raw. GDCdownloaded matrix has the gene names as rownames, TCGA barcode as colnames. At Firebrowse data, gene.id is a column and they have data information gene.id, normalized_count) along the first row.
• Firebrowse give us a .txt containing all the samples; GDC function downloads it folder per barkode.
• I downloaded by both, firebrowse data is .txt file. I read it by "read.table", saved "as.matrix", adjusted rownames, deleted first row and column, but couldn't do TCGA analysis, it gave different error messages. Does it makes sense to analyze firebrowse data with TCGAbiolinks?
• It seems for TCGAbiolinks analysis, getting the data with its' functions download data suitable for further analysis, while firebrowse data can be analyzed with different packages.

Thanks in advance.