Bioconductor Designmatrix

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limma DifferentialExpression Designmatrix

5 months ago Tadeoye ▴ 20

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453

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DESeq2 Designmatrix limma

updated 10 months ago by James W. MacDonald 68k • written 10 months ago by Neha • 0

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794

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subsettingdata edgeR designmatrix

updated 13 months ago by Gordon Smyth 52k • written 13 months ago by prity6459 • 0

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474

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limma designmatrix

updated 13 months ago by Gordon Smyth 52k • written 13 months ago by avery • 0

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1.5k

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DESeq2 designmatrix edgeR limma tidybulk

updated 2.3 years ago by Michael Love 43k • written 2.3 years ago by aditya.m ▴ 10

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1.6k

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R designmatrix edgeR limma model.matrix

2.4 years ago Abdul ▴ 20

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1.8k

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DESeq2 limma modelmatrix edgeR designmatrix

updated 3.6 years ago by Gordon Smyth 52k • written 3.6 years ago by rebecca.lea.johnston • 0

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1.5k

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designmatrix deseq2 DESeq2

updated 3.6 years ago by swbarnes2 ★ 1.4k • written 3.6 years ago by OST • 0

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1.4k

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designmatrix RNA-seq limma

updated 4.1 years ago by Gordon Smyth 52k • written 4.2 years ago by athief ▴ 20

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899

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designmatrix DifferentialExpression edgeR RNAseq

4.3 years ago • updated 4.2 years ago nageshprabhu.k ▴ 10

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1.3k

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MutlipleFactors DesignMatrix edgeR

4.3 years ago Debayan ▴ 20

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1.3k

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edgeR pairedsamples designmatrix

4.3 years ago sfidemw • 0

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1.0k

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deseq2 miRNASeq designmatrix Batch

updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by anshulmbi • 0

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edger r differentialanalysis rnaseq designmatrix

updated 6.0 years ago by Aaron Lun ★ 28k • written 6.1 years ago by Beginner ▴ 60

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1.5k

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Limma designMatrix

updated 6.9 years ago by Aaron Lun ★ 28k • written 6.9 years ago by Keifa ▴ 10

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1.6k

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limma microarray designmatrix

updated 8.8 years ago by Aaron Lun ★ 28k • written 8.8 years ago by nashchem • 0

16 results • Page 1 of 1

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Answer: Limma suqeezeVar by Gordon Smyth 52k

I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…

Comment: Discrepancies in normalised count data vs unnormalised by swbarnes2 ★ 1.4k

Well, that's going to make each sample normalize quite differently. So you should expect large difference between normalized and unnormali…

Comment: Can't install BioC packages (and manager) behind firewall by Marcel Ramos 700

Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…

Comment: Limma trend with limpa by Alejandro • 0

Dear Gordon, Thank you very much!

Answer: DESeq2 from phyloseq error by asafpr • 0

Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …

Votes

Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)

Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

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