Bioconductor Made4

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made4 plotarrays correspondence analysis ellipse

updated 8.5 years ago by Aedin Culhane ▴ 510 • written 8.8 years ago by maartenvandijk • 0

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Cancer graph made4 Cancer graph made4

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Survival hu6800 cdf probe Biobase genefilter reposTools affy affydata limma gcrma made4

updated 18.0 years ago by Ken Simpson ▴ 70 • written 18.0 years ago by Jenny Drnevich ★ 2.2k

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Classification affy made4 Classification affy made4

updated 17.4 years ago by Aedin Culhane ▴ 510 • written 17.4 years ago by Heike Pospisil ▴ 310

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affy made4 affy made4

updated 17.4 years ago by Martin Morgan 25k • written 17.4 years ago by Jenny Drnevich ★ 2.2k

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made4 made4

updated 17.6 years ago by Seth Falcon ★ 7.4k • written 17.6 years ago by Weiwei Shi ★ 1.2k

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made4 made4

updated 13.9 years ago by Steve Shen ▴ 330 • written 13.9 years ago by Rohit Farmer ▴ 170

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made4 made4

updated 12.0 years ago by Aedin Culhane ▴ 510 • written 12.0 years ago by Valerie Obenchain ★ 6.8k

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Clustering Cancer CGH GLAD made4 Clustering Cancer CGH GLAD made4

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12.0 years ago Aedin Culhane ▴ 510

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Biobase affy marray convert made4 Biobase affy marray convert made4

updated 18.4 years ago by Aedin Culhane ▴ 510 • written 18.4 years ago by Jenny Drnevich ★ 2.2k

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Clustering Cancer CGH made4 Clustering Cancer CGH made4

17.8 years ago Richard Birnie ▴ 10

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14.2 years ago xiangxue Guo ▴ 70

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12.0 years ago Barbara Bo-Ju Shih ▴ 40

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16.5 years ago Aedin Culhane ▴ 510

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made4 made4

14.2 years ago xiangxue Guo ▴ 70

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Cancer made4 ASSIGN Cancer made4 ASSIGN

14.3 years ago Steve Lianoglou ★ 13k

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made4 made4

16.9 years ago Aedin Culhane ▴ 510

18 results • Page 1 of 1

Recent ...

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Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…

Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Votes

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0