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MicroarrayData
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Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
5 weeks ago
Mj.A.
• 0
5
votes
7
replies
453
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
2
votes
6
replies
484
views
limma: vooma mean-variance trend and data filtration
MicroarrayData
limma
8 weeks ago • updated 5 weeks ago
Lily Cheang
▴ 10
0
votes
3
replies
572
views
Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData
hta20transcriptcluster.db
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
yaxade2481
• 0
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 4 months ago by
Shaimaa Gamal
• 0 • written 11 months ago by
pg45863
▴ 10
5 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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