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dss
•
reset
3
votes
0
replies
705
views
DSS : Different results between DMLtest and DMLtest.multifactor
DSS
2.7 years ago
cer.chloe
▴ 30
2
votes
4
replies
2.0k
views
Error: could not find function "DMLtest"
dss
8.1 years ago
kafkaskid
▴ 20
2
votes
4
replies
1.3k
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis
illuminaio
beadarray
DSS
bsseqData
2.3 years ago
Jojo
• 0
1
vote
1
reply
1.3k
views
Using surrogate variables as covariates in WGBS differential methylation calling
dmrseq
sva
DSS
updated 4.9 years ago by
keegan
▴ 60 • written 4.9 years ago by
gjl
▴ 10
1
vote
2
replies
1.1k
views
BUG: `showOneDMR` from DSS package creates wrong axis labels
DSS
3.4 years ago
vi.hammer
• 0
1
vote
1
reply
237
views
Question about correction of confounders for EWAS
dss
DSS
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
chuanjiao6
• 0
0
votes
0
replies
883
views
DSS DMLtest Object features
DSS
DMLtest
6.1 years ago
floriandeckert
▴ 30
0
votes
0
replies
1.2k
views
DSS DMLTest Prior Estimate of theta dispersion
DSS
dmltest
bayesian
statistics
methylation
6.1 years ago
floriandeckert
▴ 30
0
votes
6
replies
1.6k
views
limma complex contrast matrix
DSS
DSS
updated 13.1 years ago by
Ina Hoeschele
▴ 620 • written 13.1 years ago by
Prasad Siddavatam
▴ 150
0
votes
1
reply
728
views
Varying results from DSS when specifying different BSobj
DSS
DSS-single
bsseq
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
varunorama
• 0
0
votes
0
replies
884
views
[DSS] callDMR - dis.merge option does not seem to be working
DSS
bug
troubleshooting
callDMR
4.4 years ago
matthew.kearney
• 0
0
votes
0
replies
735
views
DSS smoothing RRBS and strand collapse
DSS
BSSeq
4.1 years ago
stephanie.rialle
• 0
0
votes
7
replies
2.6k
views
ERROR happens when install "DSS" package
methylationArrayAnalysis
ChAMP
DMP
DSS
updated 18 months ago by
James W. MacDonald
65k • written 24 months ago by
16301050225
• 0
0
votes
1
reply
965
views
DMRfinder findDMRs.r Error - Argument is of length zero
DSS
DMRcaller
updated 11 months ago by
Noelia
• 0 • written 21 months ago by
Claire
• 0
0
votes
0
replies
499
views
Confusing DSS outputs with smoothing (DMLtest)
DSS
13 months ago
Weisheng
• 0
0
votes
0
replies
731
views
DSS for non-CpG site analysis
DSS
methylation
4.6 years ago
CalM
• 0
0
votes
3
replies
1.7k
views
QuasiSeq vs DSS
RNASeq
Cancer
edgeR
DSS
RNASeq
Cancer
edgeR
DSS
updated 11.2 years ago by
Ryan C. Thompson
★ 7.9k • written 11.2 years ago by
Richard Friedman
★ 2.0k
0
votes
1
reply
1.4k
views
limma design matrix missing a Date column
limma
DSS
limma
DSS
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Sabet, Julia A
▴ 180
0
votes
2
replies
2.1k
views
Issue with SummarizedExperiment thru DSS::makeBSseqData
DSS
bsseq
summarizedexperiment
8.7 years ago • updated 8.6 years ago
Tim Peters
▴ 180
0
votes
1
reply
1.0k
views
DSS DMLtest with different group sizes
DSS
7.7 years ago
aerval
• 0
0
votes
0
replies
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
6.6 years ago
floriandeckert
▴ 30
21 results • Page
1 of 1
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Replies
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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Gyan Prakash Mishra
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Michael Love
42k
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Malcolm Cook
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