Bioconductor Celegans

Showing : celegans • reset

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467

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Celegans DESeq2 dds Errorinseq_len(length(idx)-1)

updated 17 months ago by James W. MacDonald 65k • written 17 months ago by Enzo.Scifo • 0

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947

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BSgenome Celegans

updated 2.0 years ago by Hervé Pagès 16k • written 2.0 years ago by Tsung-Han • 0

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1.6k

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Gviz celegans

updated 6.3 years ago by Robert Ivanek ▴ 730 • written 6.3 years ago by alex.gos90 ▴ 10

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1.4k

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biomaRt bioconductor celegans annotation

updated 6.3 years ago by Mike Smith ★ 6.5k • written 6.3 years ago by clarisbaby • 0

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745

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celegans affy convert celegans affy convert

updated 13.7 years ago by Marc Carlson ★ 7.2k • written 13.7 years ago by Julie Zhu ★ 4.3k

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967

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Transcription GO celegans BSgenome Biostrings BSgenome IRanges Transcription GO celegans

updated 14.2 years ago by Sean Davis 21k • written 14.2 years ago by Paul Shannon ★ 1.1k

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936

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celegans Biostrings celegans Biostrings

updated 15.4 years ago by Hervé Pagès 16k • written 15.4 years ago by Elizabeth Purdom ▴ 210

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847

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celegans celegans

17.1 years ago Gordon Smyth 50k

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692

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Microarray Cancer celegans drosgenome1 affy Microarray Cancer celegans drosgenome1 affy

20.6 years ago James W. MacDonald 65k

9 results • Page 1 of 1

Recent ...

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

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

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

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

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…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

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?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0