User: rachel.melamed

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Comment: C: proper transformation for differential expression in normalized log expression d
... Thanks for the reply (and for your packages).  The data are supplemental from Hoadley, et al., https://tcga-data.nci.nih.gov/docs/publications/TCGApancan_2014/rnaseq_input.txt .  They used it to cluster cancers, so maybe it made more sense for their purpose.  I have had great results using either li ...
written 4.7 years ago by rachel.melamed0
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Comment: C: proper transformation for differential expression in normalized log expression d
... Thank you!  I suspect I'm wasting my time with this data but all i have is the normalized data.  I tried vooma and it doesnt look much  better. So limma would probably give me garbage results right? Maybe some nonparametric test would work.    ...
written 4.7 years ago by rachel.melamed0
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proper transformation for differential expression in normalized log expression data
... Dear R people, I want to do an analysis of differentially expressed genes between tumor and normals.  I was hoping to start from the expression data from TCGA_PANCAN_exp_HiSeqV2_PANCAN . This contains 8415 tumor and normal data, across 27 tumor types, and I was envisioning doing some sort of anova- ...
rnaseq vsn edger deseq2 tcga written 4.7 years ago by rachel.melamed0 • updated 4.7 years ago by Gordon Smyth38k

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Popular Question 4.7 years ago, created a question with more than 1,000 views. For proper transformation for differential expression in normalized log expression data

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