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6.1k

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limma microarray block paired linear model

10.3 years ago vas ▴ 40

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3.6k

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limma covariate block paired samples technical replicates

updated 9.3 years ago by Aaron Lun ★ 28k • written 9.3 years ago by eleonoregravier ▴ 70

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9.6k

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batch effect combat limma block

updated 9.5 years ago by Ryan C. Thompson ★ 7.9k • written 9.5 years ago by eleonoregravier ▴ 70

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1.8k

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deseq2 block pca

8.7 years ago akp • 0

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2.1k

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limma block design and contrast matrix

9.7 years ago choofd • 0

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3.3k

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batch effect Coeficents non estimable block random effects limma design matrix

updated 7.4 years ago by Aaron Lun ★ 28k • written 7.4 years ago by mheydarpour ▴ 10

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2.4k

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limma microarray block

updated 18 months ago by Gordon Smyth 52k • written 6.1 years ago by tleona3 • 0

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1.3k

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diffbind block regression deseq2 chipseq

updated 4.4 years ago by Rory Stark ★ 5.2k • written 5.4 years ago by melnuesch ▴ 10

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2.3k

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limma sva block

updated 3.0 years ago by stuartthafass • 0 • written 10.4 years ago by kodream ▴ 20

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1.6k

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limma roast mroast block

updated 8.7 years ago by Ryan C. Thompson ★ 7.9k • written 8.7 years ago by barbara.shih • 0

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1.7k

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missmethyl diffvar design matrix limma block

updated 6.8 years ago by lhuang7 ▴ 50 • written 7.7 years ago by Simone ▴ 190

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1.2k

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limma BatchEffect duplicatecorrelation block batch

updated 4.3 years ago by Kevin Blighe ★ 4.0k • written 4.3 years ago by Katherine • 0

12 results • Page 1 of 1

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Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0

Thanks Michael. Just out of curiosity, would you also use the same technique for things like clustering analysis or when looking at the abn…

Comment: GAGE kegg.gsets() self-signed certificate error by Lucas • 0

Hello, I ended up solving the issue by using the first strategy: Disable the SSL certificate Verification. I used the following code to …

Comment: Clarification on GOALL / GO2ALLORFs mapping by DavideSant • 0

Thank you for your answer James. I have to disagree though, at the SGD webpage you posted there is no indication that "GO:0045719 - negati…

Comment: Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Ana by Michael Love 43k

And to add to this: when you put a generic package (e.g. DESeq2) as a tag, it actually emails the maintainer.

Answer: Using TPM from tximport of Salmon output for singscore by Michael Love 43k

TPM is fine, I've also sometimes used TPM with some robust column scaling, e.g.: ``` sf <- DESeq2::estimateSizeFactorsForMatrix(txi$abu…

Votes

Answer: Using TPM from tximport of Salmon output for singscore

Comment: Using TPM from tximport of Salmon output for singscore

Answer: affy::rma results doesn't match with ncbi website

Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types

Answer: Replicates in DESeq2

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