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Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 8 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
arfranco
▴ 130
1
vote
2
replies
249
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 13 hours ago by
Gordon Smyth
50k • written 16 hours ago by
Kim
• 0
0
votes
1
reply
46
views
package goseq seems to be not available on the latest version of R
goseq
updated 14 hours ago by
Gordon Smyth
50k • written 17 hours ago by
Patrycja
• 0
2
votes
2
replies
100
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 18 hours ago by
Michael Love
41k • written 19 hours ago by
Reza
• 0
0
votes
0
replies
31
views
Handling multiple differential expression comparisons
DESeq2
20 hours ago • updated 19 hours ago
Zainab
• 0
0
votes
0
replies
29
views
dba.plotProfile() plotting and interpretation
DiffBind
20 hours ago
Henry
▴ 10
0
votes
0
replies
70
views
Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 17 hours ago
Chris
• 0
1
vote
2
replies
276
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 17 hours ago
Kim
• 0
8 results • Page
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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!
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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