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glmTreat
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reset
6
votes
6
replies
2.9k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go
DE
edger
rnaseq
glmTreat
updated 5.4 years ago by
Gordon Smyth
52k • written 5.4 years ago by
Raito92
▴ 60
5
votes
5
replies
2.7k
views
interpreting FC values from glmTreat, especially unshrunk log-fold-changes
edgeR
glmTreat
significance testing
updated 5.8 years ago by
Yunshun Chen
▴ 900 • written 5.8 years ago by
flemi221
• 0
3
votes
3
replies
1.6k
views
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger
differential gene expression
glmtreat
updated 6.8 years ago by
Gordon Smyth
52k • written 6.9 years ago by
svlachavas
▴ 840
0
votes
5
replies
2.0k
views
glmTreat Errors for multi coefficient and analysis of deviance situations.
edgeR
glmTreat
analysis of deviance
updated 7.7 years ago by
Ryan C. Thompson
★ 7.9k • written 7.7 years ago by
BharathAnanth
▴ 80
3
votes
2
replies
1.6k
views
ROAST after edgeR glmTreat and average RPKM filter
roast
edgeR
glmtreat
updated 9.0 years ago by
Aaron Lun
★ 29k • written 9.0 years ago by
b.nota
▴ 370
1
vote
1
reply
1.3k
views
Treat p > 1
edgeR
glmTreat
updated 9.2 years ago by
Yunshun Chen
▴ 900 • written 9.2 years ago by
James W. MacDonald
68k
6 results • Page
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Answer: ROAST compare results with complex design
by
James W. MacDonald
68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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