Bioconductor Filter

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loop filter

written 6.5 years ago by kritikamish99 ▴ 10

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bioconductor mas5 perfectmatch affymetrixchip filter

updated 9.2 years ago by James W. MacDonald 65k • written 9.2 years ago by svlachavas ▴ 830

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DGElist filter edgeR

updated 6.8 years ago by Gordon Smyth 50k • written 6.8 years ago by alakatos ▴ 130

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deseq filter reads

9.3 years ago ccheung • 0

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probe filter subset gene symbol affy

9.2 years ago alakatos ▴ 130

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deseq2 filter genefilter

updated 6.4 years ago by Michael Love 41k • written 6.5 years ago by Björn • 0

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RNA WGCNA filter

4.8 years ago modarzi ▴ 10

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variantannotation vcf fixed filter

9.3 years ago Anna N. • 0

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flowcore gate subsetting filter

updated 8.6 years ago by Jiang, Mike ★ 1.3k • written 8.6 years ago by peterfoster ▴ 20

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limma filter genelist differential gene expression

updated 7.5 years ago by Gordon Smyth 50k • written 7.5 years ago by bi_Scholar • 0

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rtracklayer gff filter

updated 5.2 years ago by Michael Lawrence ★ 11k • written 5.2 years ago by alslonik • 0

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missing data filter

updated 8.4 years ago by James W. MacDonald 65k • written 8.4 years ago by rgescudero • 0

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R filter limma Normalization Microarray

12 months ago Abdul ▴ 20

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filter deseq2

updated 5.1 years ago by Michael Love 41k • written 5.1 years ago by charles.foster ▴ 160

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687

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flowCore openCyto Summary Result Filter

updated 4.0 years ago by Jake Wagner ▴ 310 • written 4.1 years ago by noviello • 0

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676

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filter deseq2

updated 12 months ago by Michael Love 41k • written 12 months ago by PD • 0

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546

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filter gate_quad_tmix gt_gating

2.1 years ago • updated 24 months ago Pierre • 0

17 results • Page 1 of 1

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Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Comment: DEseq2 coefficient by JKim • 0

Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…

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SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

Make custom Txdb class objects from Txdb

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