Bioconductor Filtering

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549

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filtering DESeq2 outliers

updated 4 months ago by Michael Love 43k • written 5 months ago by smac_head • 0

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1.8k

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filtering STD DEG limma

updated 18 months ago by Gordon Smyth 52k • written 18 months ago by alexia.brunel • 0

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1.6k

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filtering RNA-Seq CPM edgeR filterByExpr

updated 19 months ago by Gordon Smyth 52k • written 19 months ago by mohammedtoufiq91 ▴ 10

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2.4k

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expression R filtering limma

2.2 years ago • updated 2.1 years ago mohammedtoufiq91 ▴ 10

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656

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filtering probe MicroarrayData

2.3 years ago Fatemeh • 0

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2.5k

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deseq rna-seq filtering DE deseq2

updated 4.7 years ago by Michael Love 43k • written 4.7 years ago by svlachavas ▴ 840

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1.2k

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tcgabiolinks filtering gdc TCGABiolinks rnaseq

4.9 years ago jam526 • 0

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2.2k

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edger filtering

updated 6.1 years ago by Ryan C. Thompson ★ 7.9k • written 6.1 years ago by rproendo ▴ 30

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1.0k

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deseq2 filtering

updated 6.1 years ago by James W. MacDonald 67k • written 6.1 years ago by n_h_78 • 0

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1.0k

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deseq2 differential gene expression filtering

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by mnaymik • 0

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1.3k

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rna-seq filtering

updated 6.6 years ago by Gordon Smyth 52k • written 6.6 years ago by Aurora ▴ 20

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7.6k

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r edger differential gene expression filtering bioconductor

updated 6.6 years ago by Gordon Smyth 52k • written 6.6 years ago by Biologist ▴ 120

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1.7k

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edger R filtering

6.7 years ago camerond • 0

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1.4k

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DESeq2 filtering

updated 6.9 years ago by Michael Love 43k • written 6.9 years ago by A ▴ 40

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1.9k

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bed files bedtools filtering chipseq

updated 7.0 years ago by Aaron Lun ★ 28k • written 7.0 years ago by rbronste ▴ 60

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1.9k

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diffbind filtering

7.0 years ago gasta88 • 0

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1.2k

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diffbind dba.report filtering

7.1 years ago konstantopoulos • 0

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5.7k

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deseq2 filtering outliers count outliers

updated 7.4 years ago by Wolfgang Huber ★ 13k • written 7.4 years ago by heikki.sarin ▴ 10

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2.1k

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microarray affymetrix microarrays pre-filtering filtering nonspecific filtering

updated 7.6 years ago by Wolfgang Huber ★ 13k • written 7.6 years ago by n.lu • 0

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1.2k

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limma filtering

updated 7.6 years ago by Steve Lianoglou ★ 13k • written 7.6 years ago by jamie.gearing ▴ 60

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1.5k

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grangeslist filtering r

8.2 years ago Jurat Shahidin ▴ 80

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2.3k

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edger filtering cpm

updated 8.3 years ago by Gordon Smyth 52k • written 8.3 years ago by lynski008 • 0

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2.0k

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deseq2 r filtering bioconductor

updated 8.4 years ago by Steve Lianoglou ★ 13k • written 8.4 years ago by rattigak • 0

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1.2k

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filtering scran

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

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10k

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rnaseq edger filtering

updated 8.5 years ago by David ROUX ▴ 20 • written 8.6 years ago by alireza_sharifian_10 ▴ 20

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2.3k

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DEG Limma Filtering

updated 8.7 years ago by Ryan C. Thompson ★ 7.9k • written 8.8 years ago by Shamim Sarhadi ▴ 20

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2.4k

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affymetrix limma filtering

updated 9.6 years ago by James W. MacDonald 67k • written 9.6 years ago by ablanchetcohen • 0

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2.9k

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edger filtering

9.7 years ago cpcantalapiedra • 0

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2.6k

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filtering bioconductor genesymbols expressionset

9.8 years ago svlachavas ▴ 840

29 results • Page 1 of 1

Recent ...

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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40

Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …

Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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