Bioconductor Covariate

Showing : covariate • reset

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3.1k

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limma covariate block paired samples technical replicates

updated 8.4 years ago by Aaron Lun ★ 28k • written 8.4 years ago by eleonoregravier ▴ 70

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2.0k

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limma voom batcheffect covariate

updated 7.0 years ago by Gordon Smyth 50k • written 7.0 years ago by raf4 ▴ 20

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4.7k

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covariate deseqdataset Deseq2 multiple factor design

updated 8.7 years ago by Michael Love 41k • written 8.7 years ago by Lillyhchen ▴ 10

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1.5k

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limma paired covariate

updated 7.9 years ago by Steve Lianoglou ★ 13k • written 7.9 years ago by meeta.mistry ▴ 30

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1.1k

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DEG deseq2 Covariate

updated 4.9 years ago by Michael Love 41k • written 4.9 years ago by sum732 • 0

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5.1k

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limma spline design and contrast matrix covariate

updated 8.7 years ago by Aaron Lun ★ 28k • written 8.7 years ago by Hilary ▴ 30

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3.6k

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edger contrast covariate glmlrt()

7.0 years ago Jeff Skinner • 0

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4.6k

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limma reference group covariate

9.3 years ago alakatos ▴ 130

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2.5k

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limma pre/post continous covariate

8.3 years ago Smeeta Shrestha ▴ 20

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5.0k

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RNA rnaseq Covariate adjustment deseq

updated 8.2 years ago by Michael Love 41k • written 8.2 years ago by sjs0282 • 0

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1.1k

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limma covariate

updated 5.0 years ago by Gordon Smyth 50k • written 5.0 years ago by scheran02 • 0

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826

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deseq2 DEG covariate study design variables

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by Yonatan Amzaleg • 0

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2.4k

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edger differential expression covariate batch effect glm

updated 8.3 years ago by Gordon Smyth 50k • written 8.3 years ago by aec ▴ 90

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1.4k

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limma methylation R covariate MDS

updated 7.0 years ago by Aaron Lun ★ 28k • written 7.0 years ago by RC • 0

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6.4k

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limma covariate continuous categorical adjustment

updated 8.8 years ago by Gordon Smyth 50k • written 8.8 years ago by sg45653 • 0

15 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

Answer: How to retrieve gene ontology GO class from gene list?

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

Awards • All

Teacher to Gordon Smyth 50k