How to download a data matrix of gene expression data from TCGA ?

Question

[babumanish837]

Hi,

I am new in TGCA. I don't have any knowledge about it. I want to download data matrix of gene expression data for my project gene selection. I selected Home > Download Data > Data Matrix. I am selecting data expression as data types but I could not understand what I should choose in other options. I want gene expression data of different patients in different conditions/genes.

Thanks

Answer 1

[ad]

What data do you want exactly? The data matrix view offers several options allowing you to specify the types of experiments, batches, tumor/normal state etc. If you want to download data from several different types of cancer at once I don't think you should use data matrix although I've never tried to so I'm not entirely sure it couldn't be done.

[babumanish837]

@ad Thank You for your reply. I want to download gene expression data for my experiment i.e Gene Selection . I can any use any type of cancer may be colon adenocarcinoma . I want to download data for a single type of cancer that is most efficient for my project. Actually I don't have any information about which type of cancer will be most useful for my experiment.

Answer 2

[alolex]

Check out the GDAC Firehose data files for TCGA here (https://confluence.broadinstitute.org/display/GDAC/Dashboard-Stddata). Click on the "Open" links to get lists of files for each cancer type. Find the Level 3 gene expression files for the platform of interest (microarray, RNA-seq). These files are already condensed into matrix form unlike the files you get from the DataPortal (one for each patient that you have to concatenate). You can download the same file type for multiple cancers, merge them based on the gene names or probe set IDs etc to get everything in one file.