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mnncorrect
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[MnnCorrect] In case of known subpopulations
scran
single-cell
mnncorrect
rnaseq
6.8 years ago
Jens Preussner
▴ 30
5
votes
4
replies
2.0k
views
How to apply limma-trend or voom to batch corrected single cell data? (non-integer and negative values included)
MNNCorrect
scMerge
limma-trend
updated 3.0 years ago by
Gordon Smyth
50k • written 3.1 years ago by
hainct
• 0
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect
single cells
mnnCorrect
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
xingxd16
▴ 20
2
votes
2
replies
1.8k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell
scran
mnncorrect
rnaseq
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
John Reid
▴ 10
1
vote
2
replies
1.4k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN
fastMNN
mnnCorrect
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
tobi
• 0
1
vote
2
replies
2.2k
views
keep getting this error "number of rows is not the same across batches" even though my 2 matrices have the same row number
mnncorrect
batch effect
scran
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
sara.nejat
• 0
2
votes
1
reply
1.0k
views
batchelor batch correction correction runs into errors
batchelor
batch-correction
mnncorrect
fastmnn
rna-seq
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
rmf
▴ 20
6
votes
1
reply
3.1k
views
Downstream analysis after using mnnCorrect()
scran
mnncorrect
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Dave Tang
▴ 210
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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