Bioconductor Genome Data Common portal

Showing : Genome Data Common portal • reset

5

votes

9

replies

4.3k

views

TCGA Genome Data Common portal

updated 4.3 years ago by H. Z. Amini ▴ 10 • written 7.2 years ago by modarzi ▴ 10

1 result • Page 1 of 1

Recent ...

Replies

Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k

What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…

Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0

Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…

Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

Votes

Answer: Limpa Pipeline Order

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

Awards • All

Popular Question to Assa Yeroslaviz ★ 1.5k