Bioconductor Without Replicate

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limma edger timecourse without replicate voom

written 8.0 years ago by Camila Orellana ▴ 10

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720

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bsmooth without replicate dimension

6.3 years ago nilaycan • 0

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1.2k

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deseq2 time-series without replicate

updated 6.4 years ago by Michael Love 42k • written 6.4 years ago by bahlv • 0

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3.4k

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deseq2 without replicate no replicates

updated 6.5 years ago by Michael Love 42k • written 6.5 years ago by Tony • 0

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5.2k

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diffbind bioconductor differential binding analysis without replicate chipseq

7.0 years ago Hesh ▴ 10

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2.7k

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edger differential gene expression without replicate nested design help

updated 8.4 years ago by Aaron Lun ★ 28k • written 8.4 years ago by knipehf • 0

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1.5k

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edgeR differential expression without replicate

8.4 years ago gavin.oliver • 0

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1.6k

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diffbind without replicate

updated 8.7 years ago by Gord Brown ▴ 670 • written 8.7 years ago by yiweihe • 0

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3.0k

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edger without replicate

updated 8.9 years ago by Yunshun Chen ▴ 870 • written 8.9 years ago by Sushant Pawar • 0

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1.6k

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edger without replicate

updated 8.9 years ago by Aaron Lun ★ 28k • written 8.9 years ago by Sushant Pawar • 0

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5.1k

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without Replicate deseq2

updated 3.4 years ago by Michael Love 42k • written 8.9 years ago by Sushant Pawar • 0

11 results • Page 1 of 1

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Votes

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

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