Hello, I would like to perform differential gene expression analysis on ROSMAP RNA-Seq data, however, it seems like that gene expression matrix was provided in FPKMs. Since neither DESeq2 nor limma+voom() can take FPKMs as input, I would like to know 1) whether there are STAR aligned raw counts available for ROSMAP dataset; 2) If not, is there any pipeline/packages that can be applied to DE gene analysis with FPKMs? Thank you very much for your help! Wenrui

Created by Wenrui Huang wenruihuang
Hi, I'm a bit new to differential expression analysis and I have a quick question regarding the data. Is there an idkey in the dataset that would help with the design matrix? There seems to be no information provided for the sample ids.
Hi Thanneer, Thank you so much for your prompt reply! Greatly appreciated. Wenrui
Hi @wenruihuang , The star aligned ROSMAP RNA-Seq counts are here https://www.synapse.org/#!Synapse:syn8403743.

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