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vsn
•
reset
0
votes
1
reply
1.2k
views
Single channel spike in controls with custom microRNA slides - Normalization help needed
Normalization
vsn
Normalization
vsn
16.8 years ago
David
▴ 860
0
votes
0
replies
1.1k
views
Nomalization using spike-in controls in single channel arrays using limma
Normalization
vsn
Normalization
vsn
16.8 years ago
David
▴ 860
0
votes
1
reply
1.2k
views
problem with createBeadSummaryData
Normalization
vsn
Normalization
vsn
updated 16.8 years ago by
Mark Dunning
★ 1.1k • written 16.8 years ago by
Groot, Philip de
▴ 630
0
votes
0
replies
1.4k
views
SAM warning
Biophysics
Alignment
Annotation
Normalization
Cancer
hgu133plus2
probe
affy
vsn
MBCB
vsn
17.0 years ago
elliot harrison
▴ 230
0
votes
0
replies
1.0k
views
Filtering before differential expression analysis of microarrays - New paper out
Biophysics
Normalization
affy
vsn
Biophysics
Normalization
affy
vsn
17.0 years ago
Steve Lianoglou
★ 13k
0
votes
0
replies
981
views
(no subject)
Microarray
Normalization
GO
probe
vsn
limma
Microarray
Normalization
GO
probe
vsn
limma
17.0 years ago
Gordon Smyth
53k
0
votes
2
replies
2.1k
views
Can't load annotations with lumi
Microarray
OneChannel
Annotation
Normalization
probe
Biobase
annotate
genefilter
affy
vsn
updated 17.1 years ago by
Pan Du
★ 1.2k • written 17.1 years ago by
Steve Taylor
▴ 280
0
votes
1
reply
856
views
tilingArray question
vsn
vsn
updated 17.2 years ago by
Wolfgang Huber
★ 13k • written 17.2 years ago by
Anjan Purkayastha
▴ 90
0
votes
1
reply
1.7k
views
Normalization of Agilent miRNA arrays using spike-ins
miRNA
Normalization
Preprocessing
vsn
limma
miRNA
Normalization
Preprocessing
vsn
limma
updated 17.2 years ago by
Wolfgang Huber
★ 13k • written 17.2 years ago by
Christian Eisen
▴ 60
0
votes
5
replies
1.9k
views
Detection of differential expression using limma
Microarray
Normalization
vsn
limma
Microarray
Normalization
vsn
limma
updated 17.2 years ago by
Christian Eisen
▴ 10 • written 17.2 years ago by
Christian Eisen
▴ 60
0
votes
2
replies
3.2k
views
installing problem - preprocessCore, affy on linux platform
Biobase
genefilter
affy
vsn
gcrma
matchprobes
preprocessCore
Biobase
genefilter
affy
vsn
updated 17.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 17.3 years ago by
Read, Laura
▴ 20
0
votes
3
replies
1.7k
views
Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0
probe
annotate
geneplotter
affy
vsn
Ringo
probe
annotate
geneplotter
affy
vsn
Ringo
updated 17.5 years ago by
Joern Toedling
▴ 730 • written 17.5 years ago by
Ulrike Goebel
▴ 110
0
votes
1
reply
1.0k
views
Agilent single color array
Normalization
Preprocessing
vsn
limma
Normalization
Preprocessing
vsn
limma
updated 17.5 years ago by
Kasper Daniel Hansen
★ 6.5k • written 17.5 years ago by
Mark Cowley
▴ 400
0
votes
2
replies
1.7k
views
Agilent single color array
Normalization
Preprocessing
vsn
limma
Normalization
Preprocessing
vsn
limma
updated 17.5 years ago by
Sean Davis
21k • written 17.5 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
1
reply
1.4k
views
Normalization Recommendations- severe biological variation (from the digest)
Normalization
vsn
plier
Normalization
vsn
plier
updated 17.5 years ago by
Naomi Altman
★ 6.0k • written 17.5 years ago by
Nick Henriquez
▴ 20
1
vote
0
replies
794
views
Normalization Recommendations- severe biological variation
Normalization
vsn
Normalization
vsn
17.5 years ago
Siobhan A. Braybrook
▴ 60
0
votes
1
reply
1.2k
views
Input to vsn or limma of genepix file missing 635 columns
Annotation
Normalization
Biobase
affy
vsn
limma
marray
convert
Annotation
Normalization
updated 17.6 years ago by
Liolios, Konstantinos [BSD] - MED
▴ 30 • written 17.6 years ago by
Gordon Smyth
53k
0
votes
0
replies
1.9k
views
Removing control probes and treating technical replicates in Agilent one colour data
Microarray
GO
vsn
limma
Microarray
GO
vsn
limma
17.7 years ago
eldridb@stud.ntnu.no
▴ 10
0
votes
1
reply
994
views
row.names in the latest vsn
probe
vsn
probe
vsn
updated 17.8 years ago by
Roumyana Yordanova
▴ 110 • written 17.8 years ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
1.3k
views
running vsn from Limma
vsn
limma
vsn
limma
updated 17.8 years ago by
Joern Toedling
▴ 730 • written 17.8 years ago by
Catherine Juste
▴ 20
0
votes
1
reply
969
views
Update vsn: http://www.bioconductor.org/packages/devel/bioc/html/vsn.html
vsn
vsn
17.8 years ago
Roumyana Yordanova
▴ 110
0
votes
3
replies
1.5k
views
vsn with a reference set
vsn
PROcess
vsn
PROcess
updated 17.8 years ago by
Wolfgang Huber
★ 13k • written 17.8 years ago by
Roumyana Yordanova
▴ 110
0
votes
1
reply
843
views
Working with the vsn object
vsn
vsn
updated 17.8 years ago by
Wolfgang Huber
★ 13k • written 17.8 years ago by
Khan, Sohail
▴ 490
0
votes
0
replies
831
views
A couple VSN related questions
GO
Kidney
vsn
GO
Kidney
vsn
17.9 years ago
Wolfgang Huber
★ 13k
0
votes
2
replies
933
views
A couple VSN related questions
Kidney
vsn
Kidney
vsn
updated 17.9 years ago by
Wolfgang Huber
★ 13k • written 17.9 years ago by
Leo J. LEE
▴ 20
0
votes
0
replies
1.1k
views
custom affylmGUI menus
Normalization
vsn
affylmGUI
Normalization
vsn
affylmGUI
18.1 years ago
Stefanie De Bodt
▴ 10
0
votes
1
reply
765
views
VSN: narrowing down probe sets for parameter estimation
Microarray
probe
vsn
Microarray
probe
vsn
updated 18.2 years ago by
Wolfgang Huber
★ 13k • written 18.2 years ago by
Stefan Thomsen
▴ 50
0
votes
1
reply
1.4k
views
combining data from two R arrays
GO
Survival
annotate
genefilter
vsn
tilingArray
GO
Survival
annotate
genefilter
vsn
18.2 years ago
Richard Harrison
▴ 70
0
votes
2
replies
2.3k
views
Agilent 4x44 single color expression arrays
Normalization
probe
vsn
limma
gcrma
Normalization
probe
vsn
limma
gcrma
18.2 years ago
Ido M. Tamir
▴ 320
0
votes
0
replies
842
views
vsn and scaling
Normalization
vsn
Normalization
vsn
18.3 years ago
Wolfgang Huber
★ 13k
0
votes
1
reply
1.2k
views
predict vsn with reference
Microarray
affy
vsn
limma
affyio
Microarray
affy
vsn
limma
affyio
updated 18.3 years ago by
Wolfgang Huber
★ 13k • written 18.3 years ago by
chrisk
▴ 10
0
votes
2
replies
1.5k
views
vsm2
Survival
geneplotter
affy
vsn
limma
affyio
Survival
geneplotter
affy
vsn
limma
affyio
updated 18.3 years ago by
Wolfgang Huber
★ 13k • written 18.3 years ago by
Richard Harrison
▴ 70
0
votes
1
reply
1.3k
views
batch effects and VSN
Normalization
Regression
vsn
limma
oligo
Normalization
Regression
vsn
limma
oligo
updated 18.3 years ago by
Wolfgang Huber
★ 13k • written 18.3 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
2
replies
1.1k
views
Problem with "as.matrix.vsn" and "duplicateCorrelation" fromlimma
vsn
vsn
updated 18.3 years ago by
Wolfgang Huber
★ 13k • written 18.3 years ago by
Gordon Smyth
53k
0
votes
0
replies
1.9k
views
Limma: Very high logFC values
Preprocessing
probe
vsn
limma
Preprocessing
probe
vsn
limma
18.3 years ago
Gordon Smyth
53k
0
votes
1
reply
1.6k
views
globaltest - multinomial model
Survival
affy
vsn
limma
globaltest
affyio
Survival
affy
vsn
limma
globaltest
affyio
updated 18.4 years ago by
Goeman, J.J. MSTAT
▴ 150 • written 18.4 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
8
replies
4.1k
views
Reading Agilent files using read.maimages
Survival
DynDoc
genefilter
tkWidgets
affy
vsn
marray
convert
ArrayExpress
Survival
affy
updated 18.4 years ago by
Scott Reagan Franklin
▴ 20 • written 18.4 years ago by
Steve Taylor
▴ 100
0
votes
1
reply
1.2k
views
Needed help on maanova fitmaanova function
affy
vsn
limma
maanova
affyio
affy
vsn
limma
maanova
affyio
18.4 years ago
Marcelo Laia
▴ 450
0
votes
0
replies
1.5k
views
Using Ringo
Normalization
vsn
convert
Ringo
Normalization
vsn
convert
Ringo
18.4 years ago
Joern Toedling
▴ 730
0
votes
0
replies
793
views
vsn2 - update
vsn
vsn
18.6 years ago
Wolfgang Huber
★ 13k
0
votes
3
replies
1.3k
views
vsn2 bug?
Microarray
Normalization
vsn
Microarray
Normalization
vsn
updated 18.6 years ago by
Wolfgang Huber
★ 13k • written 18.6 years ago by
Tobias Straub
▴ 430
0
votes
4
replies
1.6k
views
VSN 2.2
Normalization
vsn
Normalization
vsn
updated 18.6 years ago by
Wolfgang Huber
★ 13k • written 18.7 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
2
replies
1.1k
views
getting hist(abatch) results for exprset
Normalization
affy
vsn
Normalization
affy
vsn
updated 18.7 years ago by
Sean Davis
21k • written 18.7 years ago by
Karin Lagesen
▴ 80
0
votes
0
replies
826
views
bioc-announce: vsn 2
Classification
vsn
Classification
vsn
18.8 years ago
Wolfgang Huber
★ 13k
0
votes
1
reply
734
views
expression sets with probe names
probe
vsn
probe
vsn
updated 18.8 years ago by
Wolfgang Huber
★ 13k • written 18.8 years ago by
Karin Lagesen
▴ 80
0
votes
1
reply
1.1k
views
Normalization in davidTiling demo
Normalization
GO
Survival
Biobase
genefilter
geneplotter
affy
vsn
PROcess
tilingArray
GO
updated 18.8 years ago by
Wolfgang Huber
★ 13k • written 18.8 years ago by
Julian Gehring
★ 1.3k
0
votes
0
replies
1.2k
views
What is a good method for analyzing differential expression from Illumina BeadStudio summary data?
Normalization
GO
affy
vsn
limma
beadarray
lumi
Normalization
GO
affy
vsn
limma
lumi
18.8 years ago
Gordon Smyth
53k
0
votes
1
reply
1.3k
views
Normalization in davidTiling demo
Normalization
GO
Survival
genefilter
geneplotter
affy
vsn
tilingArray
affyio
GO
Survival
updated 18.8 years ago by
Wolfgang Huber
★ 13k • written 18.8 years ago by
Julian Gehring
★ 1.3k
0
votes
0
replies
916
views
Comparing to background
Organism
vsn
limma
Organism
vsn
limma
19.1 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
999
views
Comparing to background
Organism
vsn
limma
Organism
vsn
limma
19.1 years ago
Sturgill, David NIH/NIDDK [C]
▴ 10
172 results • Page
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Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Votes
Error in SummarizedExperiment(assays = SimpleList(counts = countData)
Answer: DESeq2 class error: superclass "ExpData" not defined in the environment of the o
Limma-voom sample weights and impact on DEG numbers
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