Hi there,
I'm looking for a repository containing RNA-Seq data in a ready to analysis form (matrix with patients vs genes). I already know about TCGA, but the data there is not in a ready to process form. Does anyone know of machine learning studies that employ such kind of data and make them available in a easy to use format?
Cheers!
How about ReCount?
"ReCount is an online resource consisting of RNA-seq gene count datasets built using the raw data from 18 different studies. ... The count tables, ExpressionSets, and phenotype tables are ready to use and freely available here. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward."
If you're just looking for ready expression data to test your analysis you should definitely try Illumina Body Map Baseline Expression atlas here http://www.ebi.ac.uk/gxa/help/baseline-atlas.html.
The direct link: http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1733/E-MTAB-1733.processed.1.zip
It is tissue-specific so it would be easier to test machine learning using tissue-specific genes rather than vague cancer signatures :)
If the data is submitted with a table of RPKM expression values (or some transformation of RPKM/FPKM/TPM, etc.), then you might be able to find something like this in the series matrix file in GEO.
http://www.ncbi.nlm.nih.gov/gds/?term=RNA-Seq
Also, the published TCGA studies make your life a little easier in terms of finding the relevant data (although I don't remember if the RNA-Seq data has been concatenated into a matrix), compared to the HTTP directory:
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Thanks for the comment. However the number of cases from ReCount is still small for the kind of analysis I want to perform. Moreover, the phenotype from the studies does not seem helpful to me... I think I'll stick with TCGA data and do all the preprocessing.