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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 31 minutes ago by 50k • written 3 hours ago by • 0
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package goseq seems to be not available on the latest version of R
goseq
updated 52 minutes ago by 50k • written 4 hours ago by • 0
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Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 3 hours ago Chris • 0
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 3 hours ago Kim • 0
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 hours ago by 41k • written 5 hours ago by • 0
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Handling multiple differential expression comparisons
DESeq2
6 hours ago Zainab • 0
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dba.plotProfile() plotting and interpretation
DiffBind
7 hours ago Henry ▴ 10
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5
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 11 hours ago by 65k • written 1 day ago by ▴ 130
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 days ago • updated 14 hours ago Aurora • 0
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
8 days ago • updated 15 hours ago glaciya2018 • 0
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 20 hours ago by 50k • written 1 day ago by ▴ 10
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
You seem to have the misunderstanding that you can change the design matrix but keep all the other code unchanged. The contrasts are comput…
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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