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DSS
•
reset
3
votes
0
replies
690
views
DSS : Different results between DMLtest and DMLtest.multifactor
DSS
2.6 years ago
cer.chloe
▴ 30
2
votes
4
replies
2.0k
views
Error: could not find function "DMLtest"
dss
8.0 years ago
kafkaskid
▴ 20
2
votes
4
replies
1.2k
views
How to get methylation data in count data format from "Infinium MethylationEPIC BeadChips (Illumina)" idat files
methylationArrayAnalysis
illuminaio
beadarray
DSS
bsseqData
2.2 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 4.8 years ago by
keegan
▴ 60 • written 4.9 years ago by
gjl
▴ 10
1
vote
2
replies
1.0k
views
BUG: `showOneDMR` from DSS package creates wrong axis labels
DSS
3.4 years ago
vi.hammer
• 0
1
vote
1
reply
205
views
Question about correction of confounders for EWAS
dss
DSS
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
chuanjiao6
• 0
0
votes
0
replies
855
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
6.0 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
712
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
864
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
711
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 23 months ago by
16301050225
• 0
0
votes
1
reply
943
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
479
views
Confusing DSS outputs with smoothing (DMLtest)
DSS
12 months ago
Weisheng
• 0
0
votes
0
replies
716
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 11.1 years ago by
Ryan C. Thompson
★ 7.9k • written 11.1 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
8.6 years ago
Tim Peters
▴ 170
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
6.5 years ago
floriandeckert
▴ 30
21 results • Page
1 of 1
Recent ...
Replies
Answer: Error retrieving ensembl gene id using biomaRt...
by
Mike Smith
★ 6.5k
I think you have the assignment operator (`<-`) the wrong way round. It should be `df_biomrt_tmp <- getBM(...`
Answer: Error retrieving ensembl gene id using biomaRt...
by
James W. MacDonald
65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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