Bioconductor Gcmapweb

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rnaseq drugvsdisease gcmap gcmapweb

updated 7.6 years ago by saezrodriguez • 0 • written 7.6 years ago by bioinformatics ▴ 20

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gCMAP gCMAPWeb

9.5 years ago afshinmh • 0

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gCMAPWeb gCMAPWeb

updated 10.9 years ago by James W. MacDonald 67k • written 10.9 years ago by array chip ▴ 420

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Answer: Epic v2 Annotation CpG_maf source? by James W. MacDonald 67k

Those all come from dbSNP by way of UCSC. [See here][1], particularly lines 114 and onward. Here is no MAF for a CpG. The MAF is for the…

Comment: Deseq2 res Function by James W. MacDonald 67k

In addition to Mike's comment, do note that if you are generating a heatmap based on the set of significant genes, the direction of your co…

Answer: Struggle with the replicates of epic array data by James W. MacDonald 67k

You shouldn't be using beta values for a linear model that assumes a unimodal, untruncated distribution (beta values are strictly on (0-1) …

Comment: Identifying potentially associated gene set to drug response using GSVA by Robert Castelo ★ 3.4k

So, if I understand correctly, you derived GSVA scores from gene sets corresponding somehow to drugs in your RNA-seq data. Since GSVA score…

Answer: Deseq2 res Function by Michael Love 43k

> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…

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Answer: Deseq2 res Function

Answer: ANOVA like approach of edgeR

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