Bioconductor Filter

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967

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filter deseq2

updated 19 months ago by Michael Love 42k • written 19 months ago by PD • 0

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1.2k

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R filter limma Normalization Microarray

19 months ago Abdul ▴ 20

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689

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filter gate_quad_tmix gt_gating

2.7 years ago • updated 2.6 years ago Pierre • 0

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858

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flowCore openCyto Summary Result Filter

updated 4.5 years ago by Jake Wagner ▴ 310 • written 4.7 years ago by noviello • 0

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1.6k

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RNA WGCNA filter

5.4 years ago modarzi ▴ 10

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954

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filter deseq2

updated 5.7 years ago by Michael Love 42k • written 5.7 years ago by charles.foster ▴ 160

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1.3k

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rtracklayer gff filter

updated 5.8 years ago by Michael Lawrence ★ 11k • written 5.8 years ago by alslonik • 0

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2.0k

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deseq2 filter genefilter

updated 7.0 years ago by Michael Love 42k • written 7.1 years ago by Björn • 0

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4.1k

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loop filter

written 7.0 years ago by kritikamish99 ▴ 10

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3.6k

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DGElist filter edgeR

updated 7.4 years ago by Gordon Smyth 51k • written 7.4 years ago by alakatos ▴ 130

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1.4k

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limma filter genelist differential gene expression

updated 8.1 years ago by Gordon Smyth 51k • written 8.1 years ago by bi_Scholar • 0

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1.1k

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missing data filter

updated 9.0 years ago by James W. MacDonald 67k • written 9.0 years ago by rgescudero • 0

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1.4k

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flowcore gate subsetting filter

updated 9.2 years ago by Jiang, Mike ★ 1.3k • written 9.2 years ago by peterfoster ▴ 20

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2.9k

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probe filter subset gene symbol affy

9.7 years ago alakatos ▴ 130

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3.8k

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bioconductor mas5 perfectmatch affymetrixchip filter

updated 9.8 years ago by James W. MacDonald 67k • written 9.8 years ago by svlachavas ▴ 830

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3.3k

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deseq filter reads

9.9 years ago • updated 9.8 years ago ccheung • 0

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1.5k

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variantannotation vcf fixed filter

9.9 years ago Anna N. • 0

17 results • Page 1 of 1

Recent ...

Replies

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…

Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0

The updated version worked well on my data. Thank you!

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

Awards • All

Scholar to Haibo Liu ▴ 20