regarding gene expression data of GDAC Firehouse database

Question

[jyotsnap]

Hello guys, can i use broad gdac firehouse database normalized gene expression data directly without any preprocessing...its mRnaseq (illuminahiseq_rnaseqv2-RSEM_genes_normalized (MD5)) data, obtained from database.

[Nitin Narwade]

I think yes, why not? But what sort of analysis you are going to perform with this dataset? I mean is it comparative (normal Vs tumor, Tumor Grade etc.) OR survival?

[jyotsnap]

Thanks for reply...I am doing both differential expression analysis and survival analysis by taking these data from Broad GDAC Firehouse database, only confusion is whether i have to use them directly or any processing required, expression data file header already showing "normalized count " which means it is alredy normalized..i guess