Bioconductor Rbioinf

Showing : rbioinf • reset

1

vote

1

reply

698

views

RBioinf

updated 18 months ago by ATpoint ★ 4.9k • written 18 months ago by fr8712ca-s • 0

1

vote

2

replies

881

views

DESeq2 RBioinf

18 months ago Magdalena • 0

2

votes

6

replies

5.2k

views

RBioinf

3.7 years ago bbhatt • 0

3 results • Page 1 of 1

Recent ...

Replies

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…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

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

Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```

Votes

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

Awards • All