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genespring
•
reset
2
votes
1
reply
3.8k
views
RNA-seq Differential expression using 3 groups
rnaseq
anova
deseq2
edger
genespring
9.5 years ago
BM
• 0
0
votes
2
replies
2.4k
views
First time use of limma for two-color agilent array analysis
qPCR
limma
GeneSpring
qPCR
limma
GeneSpring
updated 10.9 years ago by
James W. MacDonald
67k • written 10.9 years ago by
Calin-Jageman, Robert
▴ 30
0
votes
4
replies
2.0k
views
Should AgiMicroRna and GeneSpring quantile normalisation be the same ?
Normalization
GeneSpring
microRNA
AgiMicroRna
Normalization
GeneSpring
microRNA
AgiMicroRna
updated 12.5 years ago by
Paul Geeleher
★ 1.3k • written 12.5 years ago by
Seyit Ali KAYIS
▴ 30
0
votes
0
replies
1.1k
views
Limma package for Agilent microarray Image Analysis
limma
GeneSpring
limma
GeneSpring
13.0 years ago
Karthik K N
▴ 200
0
votes
0
replies
1.2k
views
miRNA array normalization - RMA vs Genespring comparison
miRNA
Normalization
GeneSpring
miRNA
Normalization
GeneSpring
13.0 years ago
Andrea Grilli
▴ 240
0
votes
0
replies
1.1k
views
Difference between LIMMA and Genespring
Microarray
Genetics
limma
GeneSpring
Microarray
Genetics
limma
GeneSpring
13.1 years ago
Gordon Smyth
52k
0
votes
1
reply
1.5k
views
Difference between LIMMA and Genespring
limma
GeneSpring
limma
GeneSpring
updated 13.2 years ago by
Edwin Groot
▴ 230 • written 13.2 years ago by
Jin, Ming
▴ 10
0
votes
1
reply
3.2k
views
2 way anova in Bioconductor
Microarray
GO
genefilter
limma
GeneSpring
ABarray
preprocessCore
arrayQualityMetrics
BRAIN
updated 13.6 years ago by
Guillaume Meurice
▴ 210 • written 13.6 years ago by
Dana.Stanley@csiro.au
▴ 110
0
votes
6
replies
2.2k
views
2 way anova in Bioconductor
GO
genefilter
limma
GeneSpring
ABarray
preprocessCore
arrayQualityMetrics
GO
genefilter
updated 13.6 years ago by
Jenny Drnevich
★ 2.0k • written 13.6 years ago by
Dana.Stanley@csiro.au
▴ 110
0
votes
0
replies
974
views
agilent shRNA library
Microarray
GeneSpring
Microarray
GeneSpring
14.4 years ago
Giusy Della Gatta
▴ 50
0
votes
4
replies
1.4k
views
How to cope with arrays hybridized at significantly different time.
GeneSpring
GeneSpring
updated 15.9 years ago by
Steve Lianoglou
★ 13k • written 15.9 years ago by
Paparountas Triantafyllos
▴ 40
0
votes
0
replies
692
views
export toptables into Genespring
limma
GeneSpring
limma
GeneSpring
16.3 years ago
Pemmasani, Kalyani
▴ 10
0
votes
1
reply
2.2k
views
what is the best baseline transformation method before clustering
GO
Clustering
probe
affy
gcrma
GeneSpring
GO
Clustering
probe
affy
gcrma
GeneSpring
updated 16.4 years ago by
Sean Davis
21k • written 16.4 years ago by
Ruppert Valentino
▴ 270
0
votes
3
replies
1.2k
views
Missing ProbeSets in Affymetrix MoGene 1.0 ST chips
Annotation
cdf
GeneSpring
Annotation
cdf
GeneSpring
updated 16.4 years ago by
James W. MacDonald
67k • written 16.4 years ago by
Mark Cowley
▴ 910
0
votes
2
replies
1.3k
views
Agilent MAGE-ML
RMAGEML
GeneSpring
PROcess
RMAGEML
GeneSpring
PROcess
updated 16.5 years ago by
Martin Morgan
25k • written 16.5 years ago by
gabriele bucci
▴ 10
0
votes
7
replies
16k
views
How to adjust the Heatmap.2 color key
Microarray
GeneSpring
Microarray
GeneSpring
16.6 years ago
Martin Bonke
▴ 40
0
votes
0
replies
1.7k
views
Cutoff to use for IQR filtering in genefilter
genefilter
affy
limma
GeneSpring
affylmGUI
GLAD
SIM
genefilter
affy
limma
GeneSpring
16.6 years ago
Mark Cowley
▴ 400
0
votes
1
reply
1.2k
views
How to calculate the values lige GeneSpring from the raw intensities (Agilent)
GeneSpring
GeneSpring
updated 16.6 years ago by
Mark Cowley
▴ 400 • written 16.6 years ago by
olszewski@atlas-biolabs.de
▴ 30
0
votes
2
replies
1.3k
views
Do my Limma results look "normal"?
Microarray
Cancer
Breast
limma
GeneSpring
Microarray
Cancer
Breast
limma
GeneSpring
updated 16.7 years ago by
Paul Geeleher
★ 1.3k • written 16.7 years ago by
Gordon Smyth
52k
0
votes
2
replies
1.4k
views
Do my Limma results look "normal"?
Microarray
Cancer
Breast
limma
GeneSpring
Microarray
Cancer
Breast
limma
GeneSpring
updated 16.7 years ago by
rgentleman
★ 5.5k • written 16.7 years ago by
Paul Geeleher
★ 1.3k
0
votes
3
replies
1.4k
views
limma - Considering Batch Effect
limma
GeneSpring
limma
GeneSpring
updated 17.5 years ago by
James W. MacDonald
67k • written 17.5 years ago by
Nathan Haigh
▴ 120
0
votes
1
reply
827
views
Interface to BASE microarray data
Microarray
Cancer
GeneSpring
Microarray
Cancer
GeneSpring
updated 18.6 years ago by
Henrik Bengtsson
★ 2.4k • written 18.6 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
1.2k
views
MLInterfaces
GeneSpring
MLInterfaces
GeneSpring
MLInterfaces
updated 18.9 years ago by
Stephen Henderson
★ 1.0k • written 18.9 years ago by
Qi.Zhang@astrazeneca.com
▴ 60
0
votes
3
replies
1.3k
views
Rocke-Lorenzato model or Global Error Model in Bioconductor
GeneSpring
GeneSpring
updated 19.2 years ago by
Norman Pavelka
▴ 190 • written 19.2 years ago by
Ruppert Valentino
▴ 270
0
votes
2
replies
1.5k
views
limma Normalization question
Genetics
Normalization
limma
GeneSpring
limmaGUI
Genetics
Normalization
limma
GeneSpring
19.2 years ago
Gordon Smyth
52k
0
votes
0
replies
1.1k
views
limma Normalization question
Genetics
Normalization
limma
GeneSpring
limmaGUI
Genetics
Normalization
limma
GeneSpring
19.2 years ago
Cecilia McGregor
▴ 110
0
votes
2
replies
1.4k
views
GeneSpring can call R functions?
GO
GeneSpring
safe
GO
GeneSpring
safe
updated 19.7 years ago by
Ramon Diaz
★ 1.1k • written 19.7 years ago by
Ken Termiso
▴ 250
0
votes
0
replies
1.0k
views
JOB: Research Associate at Texas A&M
Clustering
GeneSpring
Clustering
GeneSpring
19.9 years ago
Marina Vannucci
▴ 20
0
votes
0
replies
808
views
affylmGUI - feedback, questions
gcrma
GeneSpring
affylmGUI
gcrma
GeneSpring
affylmGUI
20.0 years ago
SteffenMöller
▴ 30
0
votes
0
replies
822
views
Could limma be as good as GeneSpring in nomalization?
Genetics
limma
GeneSpring
Genetics
limma
GeneSpring
20.2 years ago
donghu@itsa.ucsf.edu
▴ 70
0
votes
0
replies
1.0k
views
Could limma be as good as GeneSpring in normalization?
Microarray
Genetics
limma
GeneSpring
Microarray
Genetics
limma
GeneSpring
20.2 years ago
Elizabeth Brooke-Powell
▴ 160
0
votes
0
replies
788
views
Error encountered while using RMA
Normalization
GeneSpring
Normalization
GeneSpring
20.3 years ago
Madeleine Gross
▴ 10
0
votes
0
replies
895
views
What to do about the missing probe sequences for HG_U95A?
Normalization
GO
probe
affy
GeneSpring
Normalization
GO
probe
affy
GeneSpring
20.3 years ago
Thon de Boer
▴ 10
0
votes
2
replies
1.3k
views
som - can it divide the samples into clusters
GeneSpring
GeneSpring
20.5 years ago
Liu, Xin
▴ 120
0
votes
0
replies
996
views
GeneSpring package usage
GeneSpring
GeneSpring
20.5 years ago
marchiem@libero.it
▴ 150
0
votes
1
reply
870
views
maPrintTip confusion
GO
GeneSpring
ASSIGN
GO
GeneSpring
ASSIGN
updated 20.6 years ago by
Jean Yee Hwa Yang
▴ 920 • written 20.7 years ago by
Alison Wise
▴ 10
0
votes
0
replies
787
views
Normalization with common reference
Normalization
Cancer
vsn
GeneSpring
Normalization
Cancer
vsn
GeneSpring
20.7 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
1.3k
views
median polish vs mas/PLIER info
Microarray
Normalization
Cancer
probe
affy
GeneSpring
PROcess
plier
Microarray
Cancer
20.7 years ago
Anthony Bosco
▴ 500
0
votes
0
replies
1.4k
views
MAS vs gcrma, rma and Li-Wong method in Affy package for TC study
Normalization
Clustering
affy
gcrma
GeneSpring
Normalization
Clustering
affy
gcrma
20.9 years ago
Lizhe Xu
▴ 210
0
votes
2
replies
1.6k
views
warning messages in gcrma
Microarray
Normalization
Cancer
moe430a
moe430b
cdf
probe
affy
gcrma
siggenes
GeneSpring
updated 20.9 years ago by
James W. MacDonald
67k • written 20.9 years ago by
Lizhe Xu
▴ 210
0
votes
1
reply
1.1k
views
questions about Affy package from new user: onemore question
Microarray
Normalization
Cancer
affy
GeneSpring
Microarray
Normalization
Cancer
affy
updated 20.9 years ago by
James W. MacDonald
67k • written 20.9 years ago by
Lizhe Xu
▴ 210
0
votes
0
replies
1.0k
views
FW: questions about Affy package from new user: onemore question
Microarray
Normalization
Cancer
affy
GeneSpring
Microarray
Normalization
Cancer
affy
20.9 years ago
Lizhe Xu
▴ 210
0
votes
1
reply
849
views
questions about Affy package from new user: one more question
Microarray
Normalization
Cancer
GeneSpring
Microarray
Normalization
Cancer
GeneSpring
updated 20.9 years ago by
Adaikalavan Ramasamy
★ 1.8k • written 20.9 years ago by
James W. MacDonald
67k
0
votes
0
replies
839
views
very small fold change from RMA data
affy
GeneSpring
affy
GeneSpring
21.2 years ago
Qiang Li
▴ 10
0
votes
1
reply
1.2k
views
very small fold change from RMA data
affy
GeneSpring
affy
GeneSpring
updated 21.3 years ago by
Wolfgang Huber
★ 13k • written 21.3 years ago by
Dapeng Cui
▴ 40
0
votes
1
reply
1.2k
views
RMA and GeneSpring?
Normalization
affy
GeneSpring
Normalization
affy
GeneSpring
updated 21.3 years ago by
Fátima Núñez
▴ 130 • written 21.3 years ago by
Dapeng Cui
▴ 40
0
votes
0
replies
782
views
Getting unmodified Affy-Data via R+ and the Affy package...
GeneSpring
GeneSpring
21.9 years ago
Joern Wessels
▴ 20
0
votes
2
replies
1.2k
views
RMA results
affy
GeneSpring
affy
GeneSpring
updated 22.0 years ago by
Oliver Hartmann
▴ 70 • written 22.1 years ago by
Duhaime Johanne
▴ 100
0
votes
4
replies
1.2k
views
R and GeneSpring
GeneSpring
GeneSpring
updated 22.7 years ago by
Anthony Rossini
▴ 530 • written 22.7 years ago by
Jess Mar
▴ 20
49 results • Page
1 of 1
Recent ...
Replies
Answer: Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes
by
James W. MacDonald
67k
This support site is meant to provide support for Bioconductor packages, but `Meffil` is not part of Bioconductor. You could presumably con…
Comment: Unused arguments error without used arguments in GSVA?
by
Axel Klenk
★ 1.1k
> It looks like the ssgseaParam function might not be passing the > correct parameters to GSVA::gsva() Apparently because of the extra com…
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
by
franknappi14
• 0
I tried it and it's working properly.
Answer: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
by
ATpoint
★ 4.6k
The vignette covers batch effects as per the authors best practice, please read it and consider following it.
Comment: DESeq2 analysis with transcript counts
by
kahunroleh
• 0
Thanks for sharing the solution. I also face this problem. [nulls][1] [1]: https://nulls-brawl-apk.fr/
Votes
Answer: Reducing and aggregating GRanges with gaps using plyranges
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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