Bioconductor Variancepartition

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variancePartition

6 days ago Le • 0

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variancePartition BiocParallel

4 months ago hayleyw • 0

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variancePartition RNASeqData limma BulkRNAseq RNASeq

updated 4 months ago by Gordon Smyth 50k • written 6 months ago by Gimena • 0

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variancePartition mixedmodel dream

8 months ago hayleyw • 0

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DESeq2 variancePartition

13 months ago • updated 12 months ago Weiqian ▴ 10

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RNAseq variancePartition edgeR dream

13 months ago DH • 0

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variancePa variancePartition limma-voom dream

updated 13 months ago by Gordon Smyth 50k • written 14 months ago by Le • 0

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expression variancePartition edgeR

20 months ago Jonathan • 0

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edgeR limma variancePartition

updated 2.8 years ago by Gordon Smyth 50k • written 2.8 years ago by jackgisby • 0

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limma variancePartition

updated 2.8 years ago by Gordon Smyth 50k • written 2.8 years ago by jarod ▴ 30

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variancePartition limma

3.0 years ago Junghoon ▴ 10

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variancePartition limma BiocParallel

3.0 years ago Junghoon ▴ 10

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BiocParallel limma variancePartition

3.0 years ago • updated 2.8 years ago Junghoon ▴ 10

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dream variancePartition limma differential expression repeated measures

updated 4.5 years ago by Gordon Smyth 50k • written 4.6 years ago by hermidalc ▴ 20

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variancepartition lme4 mixedmodel

updated 4.6 years ago by gabriel.hoffman ▴ 110 • written 4.7 years ago by c.taylor • 0

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limma voom variancePartition dream

updated 4.6 years ago by gabriel.hoffman ▴ 110 • written 4.8 years ago by Ben ▴ 50

16 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Answer: Log-cpm values from limma

Awards • All

Supporter to Jonathan ▴ 10