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Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.2k
It's perfectly confounded, you cannot correct for anything. Nothing will ever change that. People are just ignoring this simple fact becaus…
Comment: How should I run ssGSEA Hallmark Enrichment Analysis?
by
Tanvi
• 0
Hi, a follow up for your question, have you tried using fgsea library for the ssGSEA analysis or did you directly use gsva? I am particular…
Answer: Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connec
by
Mike Smith
★ 6.5k
Thank you for reporting this. There seemed to be an issue where the list of available filters returned by the BioMart server when using th…
Answer: PCA (Principal Component Analysis) plots from ChIP-seq data
by
egbastakis
• 0
Hi ATpoint, Many thanks for your explanation, and for your suggestions as well.
Comment: Too many significant genes when integrating gtex and tcga
by
manwar
• 0
Its true, however, there are many cancers in TCGA that do not have normal samples and in that case, someone can borrow normal samples from …
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Answer: Warning message when running limma with covariates
Answer: Warning message when running limma with covariates
Comment: Limma with covariates
Answer: Limma with covariates
A: How to use GenomicRanges to find overlaps by percentage covered of interval
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