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limmaGUI
•
reset
0
votes
9
replies
1.9k
views
Getting LimmaGUI to run
tkWidgets
widgetTools
limmaGUI
widgetInvoke
tkWidgets
widgetTools
limmaGUI
widgetInvoke
18.8 years ago
chris umbricht
▴ 110
2
votes
6
replies
1.1k
views
Limma beta coefficient confidence intervals
limma
limmaGUI
beta
22 months ago
fluentin44
• 0
0
votes
6
replies
1.4k
views
LimmaGUI Spot Quality
limmaGUI
limmaGUI
updated 19.8 years ago by
Gordon Smyth
50k • written 19.8 years ago by
Elizabeth Brooke-Powell
▴ 160
3
votes
6
replies
6.6k
views
Unable to install "limma" package on RStudio
Bioconductor
limma
limmaGUI
2.2 years ago
jaydengitt
• 0
0
votes
6
replies
2.2k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
affylmGUI
limmaGUI
affylmGUI
limmaGUI
updated 15.7 years ago by
ilhami visne
▴ 10 • written 15.8 years ago by
Deanne Taylor
▴ 50
2
votes
5
replies
1.7k
views
NA coefficients values for samples with all zeros
limmagui
proteomics
8.4 years ago
vedran.franke
• 0
1
vote
5
replies
2.8k
views
Using Limma for proteomics (2D DIGE) datasets
Proteomics
limma
impute
limmaGUI
Proteomics
limma
impute
limmaGUI
updated 8.8 years ago by
sm
• 0 • written 14.5 years ago by
Tom Wenseleers
▴ 60
1
vote
5
replies
1.0k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI
normalization
limma
voom
Normalization
updated 9 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
0
votes
4
replies
1.0k
views
LimmaGUI discards spots with no signal on one channel?
limma
limmaGUI
limma
limmaGUI
19.1 years ago
Gordon Smyth
50k
1
vote
4
replies
404
views
limma design model for categorical variable
DNAMethylation
limmaGUI
biostatistics
limma
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
Jitendra
▴ 10
0
votes
4
replies
1.4k
views
getting normexp (and log2 transformed) values - not further-processed M values
Microarray
limma
limmaGUI
Microarray
limma
limmaGUI
14.6 years ago
adoty@umd.edu
▴ 30
0
votes
4
replies
1.1k
views
BlueFuse in limmaGUI [was LimmaGUI Error]
Normalization
GO
limmaGUI
ASSIGN
Normalization
GO
limmaGUI
ASSIGN
updated 18.8 years ago by
Brooke-Powell, Elizabeth
▴ 170 • written 18.8 years ago by
Gordon Smyth
50k
6
votes
4
replies
985
views
Limma prametrization
limm
MathematicalBiology
limmaGUI
StatisticalMethod
2.3 years ago
Giovanni
• 0
0
votes
3
replies
1.3k
views
duplicate correlation of 4 "within array replicates" limmaGUI
GUI
limma
limmaGUI
microRNA
GUI
limma
limmaGUI
microRNA
15.6 years ago
Gordon Smyth
50k
0
votes
3
replies
2.2k
views
Limma: background correction. Use or ignore?
Microarray
Cancer
affy
limma
limmaGUI
Microarray
Cancer
affy
limma
limmaGUI
updated 18.1 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k • written 18.1 years ago by
Gordon Smyth
50k
0
votes
3
replies
1.2k
views
spot filtering
limma
limmaGUI
limma
limmaGUI
updated 18.8 years ago by
michael watson IAH-C
★ 3.4k • written 18.8 years ago by
Brooke-Powell, Elizabeth
▴ 170
0
votes
3
replies
1.3k
views
limma: print-tip loess and empty spots
Normalization
GO
GUI
limma
limmaGUI
Normalization
GO
GUI
limma
limmaGUI
16.9 years ago
Gordon Smyth
50k
0
votes
3
replies
1.4k
views
LimmaGUI Error
Normalization
GO
limmaGUI
ASSIGN
Normalization
GO
limmaGUI
ASSIGN
18.8 years ago
Brooke-Powell, Elizabeth
▴ 170
0
votes
3
replies
2.0k
views
Limma: correct calculation of B statistics (log odds)
limma
limmaGUI
limma
limmaGUI
updated 18.0 years ago by
Wittner, Ben
▴ 290 • written 18.0 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k
1
vote
3
replies
3.5k
views
Limma: correct calculation of B statistics (log odds)
Microarray
Genetics
limma
limmaGUI
Microarray
Genetics
limma
limmaGUI
updated 18.0 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k • written 18.0 years ago by
Gordon Smyth
50k
1
vote
3
replies
343
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 22 days ago by
Simran
• 0
0
votes
2
replies
2.2k
views
problem with tkrplot installation
limmaGUI
limmaGUI
updated 15.7 years ago by
James W. MacDonald
65k • written 15.7 years ago by
A Yulandi
▴ 20
0
votes
2
replies
1.3k
views
"limma" and "Imagene"
GUI
limma
limmaGUI
GUI
limma
limmaGUI
updated 19.8 years ago by
Gordon Smyth
50k • written 19.8 years ago by
Breuk102
▴ 50
0
votes
2
replies
875
views
Problem loading files into limmaGUI
limma
limmaGUI
limma
limmaGUI
updated 19.9 years ago by
Gordon Smyth
50k • written 19.9 years ago by
Elva Diaz
▴ 10
0
votes
2
replies
1.4k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
affylmGUI
limmaGUI
affylmGUI
limmaGUI
updated 15.8 years ago by
Ross Lazarus
▴ 90 • written 15.8 years ago by
Jarno Tuimala
▴ 140
0
votes
2
replies
1.2k
views
limmaGUI: target file and spot file
limmaGUI
limmaGUI
updated 15.8 years ago by
Mark Cowley
▴ 910 • written 15.8 years ago by
Jamila Bernardi
▴ 10
0
votes
2
replies
852
views
Fwd: Getting LimmaGUI to run
limmaGUI
limmaGUI
updated 18.8 years ago by
Rob J Goedman
▴ 40 • written 18.8 years ago by
chris umbricht
▴ 110
0
votes
2
replies
287
views
limma model matrix questions
limmaGUI
limma
pairedsamples
10 weeks ago
whyw6948
• 0
0
votes
2
replies
888
views
How to do normalization without background subtraction in limmaGUI or limma?
Normalization
limmaGUI
Normalization
limmaGUI
updated 20.5 years ago by
Gordon Smyth
50k • written 20.5 years ago by
ying chen
▴ 40
1
vote
2
replies
966
views
Limma adj.p.value the same for many different p.values
limmaGUI
limma
adj.p.value
StatisticalMethod
19 months ago
walkerrh95
• 0
0
votes
2
replies
984
views
Limma: background correction. Use or ignore?
limmaGUI
limmaGUI
updated 18.1 years ago by
James W. MacDonald
65k • written 18.1 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k
0
votes
2
replies
952
views
Limma and limmaGUI with Imagene files, problems/bugs report
limma
limmaGUI
ASSIGN
limma
limmaGUI
ASSIGN
updated 19.4 years ago by
Gordon Smyth
50k • written 19.4 years ago by
Breuk102
▴ 50
0
votes
2
replies
2.3k
views
limma, spot and technical replicates
Genetics
limma
limmaGUI
Genetics
limma
limmaGUI
updated 18.5 years ago by
STKH Steen Krogsgaard
▴ 150 • written 18.5 years ago by
Cecilia McGregor
▴ 110
0
votes
2
replies
796
views
gcrma in affylmGUI
gcrma
limmaGUI
gcrma
limmaGUI
updated 19.9 years ago by
James Wettenhall
▴ 1000 • written 20.0 years ago by
Luckey, John
▴ 90
0
votes
2
replies
1.2k
views
limmaGUI: Warning: ActiveTcl could not be found....
limmaGUI
limmaGUI
updated 20.6 years ago by
A.J. Rossini
▴ 810 • written 20.6 years ago by
Marcelo Luiz de Laia
▴ 770
0
votes
2
replies
1.1k
views
limmaGUI: Warning: ActiveTcl could not be found...
limmaGUI
limmaGUI
updated 20.6 years ago by
Marcelo Luiz de Laia
▴ 770 • written 20.6 years ago by
James Wettenhall
▴ 1000
0
votes
2
replies
900
views
LimmaGUI Background corrections
limmaGUI
limmaGUI
updated 19.7 years ago by
Gordon Smyth
50k • written 19.7 years ago by
Elizabeth Brooke-Powell
▴ 160
0
votes
2
replies
1.1k
views
help for limmaGUI
Microarray
limmaGUI
Microarray
limmaGUI
updated 16.9 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k • written 16.9 years ago by
Ziping Zhang
▴ 10
0
votes
2
replies
1.2k
views
limma Normalization question
Genetics
Normalization
limma
GeneSpring
limmaGUI
Genetics
Normalization
limma
GeneSpring
18.5 years ago
Gordon Smyth
50k
0
votes
2
replies
1.2k
views
problem detected during utilization of LimmaGUI
Microarray
limmaGUI
Microarray
limmaGUI
updated 14.4 years ago by
Seth Falcon
★ 7.4k • written 14.4 years ago by
Susana Gomes
▴ 10
0
votes
1
reply
848
views
LimmaGUI and limma
limma
limmaGUI
limma
limmaGUI
updated 19.7 years ago by
James Wettenhall
▴ 1000 • written 19.7 years ago by
Binita Dutta
▴ 100
0
votes
1
reply
904
views
limmaGUI and Agilent output files!
Microarray
limmaGUI
Microarray
limmaGUI
updated 19.8 years ago by
James Wettenhall
▴ 1000 • written 19.8 years ago by
Adrian Peres
▴ 30
0
votes
1
reply
791
views
Setting the spacing between duplicates in limmaGUI
limmaGUI
limmaGUI
updated 20.6 years ago by
Gordon Smyth
50k • written 20.6 years ago by
Peter Baker CMIS, Indooroopilly
▴ 80
0
votes
1
reply
958
views
LimmaGUI
limmaGUI
limmaGUI
updated 20.2 years ago by
James W. MacDonald
65k • written 20.2 years ago by
Binita Dutta
▴ 100
0
votes
1
reply
1.5k
views
Analysis Interface Projects
limma
limmaGUI
limma
limmaGUI
updated 20.7 years ago by
Dave Waddell
▴ 160 • written 20.7 years ago by
James Wettenhall
▴ 1000
0
votes
1
reply
2.0k
views
Limma user’s guide example data sets
Microarray
limma
limmaGUI
weaver
Microarray
limma
limmaGUI
weaver
updated 15.9 years ago by
Wang, Jixin
▴ 130 • written 15.9 years ago by
Keith Satterley
▴ 450
0
votes
1
reply
1.1k
views
Re: Limma GUI exporting
Microarray
limma
affylmGUI
limmaGUI
Microarray
limma
affylmGUI
limmaGUI
19.9 years ago
James Wettenhall
▴ 1000
0
votes
1
reply
1.2k
views
One-Color Agilent Data into Limma GUI
GO
limma
limmaGUI
GO
limma
limmaGUI
updated 16.6 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k • written 16.6 years ago by
elliot harrison
▴ 230
0
votes
1
reply
1.1k
views
asMatrixWeights: weights of unexpected shape
GUI
limma
limmaGUI
GUI
limma
limmaGUI
updated 15.6 years ago by
Christine Voellenkle
▴ 90 • written 15.6 years ago by
Gordon Smyth
50k
0
votes
1
reply
1.6k
views
statistics for differential expression: adjusted p-values<0.05 BUT negative B-odds?
Normalization
limma
limmaGUI
Normalization
limma
limmaGUI
updated 15.5 years ago by
Paolo Innocenti
▴ 320 • written 15.5 years ago by
Christine Voellenkle
▴ 90
50 results • Page
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Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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