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genespring
•
reset
0
votes
7
replies
16k
views
How to adjust the Heatmap.2 color key
Microarray
GeneSpring
Microarray
GeneSpring
15.9 years ago
Martin Bonke
▴ 40
2
votes
1
reply
3.5k
views
RNA-seq Differential expression using 3 groups
rnaseq
anova
deseq2
edger
genespring
8.8 years ago
BM
• 0
0
votes
1
reply
3.0k
views
2 way anova in Bioconductor
Microarray
GO
genefilter
limma
GeneSpring
ABarray
preprocessCore
arrayQualityMetrics
BRAIN
updated 12.9 years ago by
Guillaume Meurice
▴ 210 • written 12.9 years ago by
Dana.Stanley@csiro.au
▴ 110
0
votes
2
replies
2.2k
views
First time use of limma for two-color agilent array analysis
qPCR
limma
GeneSpring
qPCR
limma
GeneSpring
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Calin-Jageman, Robert
▴ 30
0
votes
6
replies
2.0k
views
2 way anova in Bioconductor
GO
genefilter
limma
GeneSpring
ABarray
preprocessCore
arrayQualityMetrics
GO
genefilter
updated 12.9 years ago by
Jenny Drnevich
★ 2.0k • written 12.9 years ago by
Dana.Stanley@csiro.au
▴ 110
0
votes
1
reply
1.9k
views
what is the best baseline transformation method before clustering
GO
Clustering
probe
affy
gcrma
GeneSpring
GO
Clustering
probe
affy
gcrma
GeneSpring
updated 15.7 years ago by
Sean Davis
21k • written 15.7 years ago by
Ruppert Valentino
▴ 270
0
votes
4
replies
1.7k
views
Should AgiMicroRna and GeneSpring quantile normalisation be the same ?
Normalization
GeneSpring
microRNA
AgiMicroRna
Normalization
GeneSpring
microRNA
AgiMicroRna
updated 11.8 years ago by
Paul Geeleher
★ 1.3k • written 11.8 years ago by
Seyit Ali KAYIS
▴ 30
0
votes
0
replies
1.6k
views
Cutoff to use for IQR filtering in genefilter
genefilter
affy
limma
GeneSpring
affylmGUI
GLAD
SIM
genefilter
affy
limma
GeneSpring
15.9 years ago
Mark Cowley
▴ 400
0
votes
2
replies
1.4k
views
warning messages in gcrma
Microarray
Normalization
Cancer
moe430a
moe430b
cdf
probe
affy
gcrma
siggenes
GeneSpring
updated 20.2 years ago by
James W. MacDonald
65k • written 20.2 years ago by
Lizhe Xu
▴ 210
0
votes
1
reply
1.4k
views
Difference between LIMMA and Genespring
limma
GeneSpring
limma
GeneSpring
updated 12.4 years ago by
Edwin Groot
▴ 230 • written 12.4 years ago by
Jin, Ming
▴ 10
0
votes
0
replies
1.2k
views
MAS vs gcrma, rma and Li-Wong method in Affy package for TC study
Normalization
Clustering
affy
gcrma
GeneSpring
Normalization
Clustering
affy
gcrma
20.1 years ago
Lizhe Xu
▴ 210
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
3
replies
1.2k
views
limma - Considering Batch Effect
limma
GeneSpring
limma
GeneSpring
updated 16.8 years ago by
James W. MacDonald
65k • written 16.8 years ago by
Nathan Haigh
▴ 120
0
votes
4
replies
1.2k
views
How to cope with arrays hybridized at significantly different time.
GeneSpring
GeneSpring
updated 15.2 years ago by
Steve Lianoglou
★ 13k • written 15.2 years ago by
Paparountas Triantafyllos
▴ 40
0
votes
2
replies
1.2k
views
GeneSpring can call R functions?
GO
GeneSpring
safe
GO
GeneSpring
safe
updated 19.0 years ago by
Ramon Diaz
★ 1.1k • written 19.0 years ago by
Ken Termiso
▴ 250
0
votes
2
replies
1.2k
views
Agilent MAGE-ML
RMAGEML
GeneSpring
PROcess
RMAGEML
GeneSpring
PROcess
updated 15.8 years ago by
Martin Morgan
25k • written 15.8 years ago by
gabriele bucci
▴ 10
0
votes
0
replies
1.2k
views
median polish vs mas/PLIER info
Microarray
Normalization
Cancer
probe
affy
GeneSpring
PROcess
plier
Microarray
Cancer
20.0 years ago
Anthony Bosco
▴ 500
0
votes
2
replies
1.1k
views
Do my Limma results look "normal"?
Microarray
Cancer
Breast
limma
GeneSpring
Microarray
Cancer
Breast
limma
GeneSpring
updated 16.0 years ago by
rgentleman
★ 5.5k • written 16.0 years ago by
Paul Geeleher
★ 1.3k
0
votes
2
replies
1.1k
views
Do my Limma results look "normal"?
Microarray
Cancer
Breast
limma
GeneSpring
Microarray
Cancer
Breast
limma
GeneSpring
updated 16.0 years ago by
Paul Geeleher
★ 1.3k • written 16.0 years ago by
Gordon Smyth
50k
0
votes
2
replies
1.1k
views
som - can it divide the samples into clusters
GeneSpring
GeneSpring
19.8 years ago
Liu, Xin
▴ 120
0
votes
3
replies
1.1k
views
Rocke-Lorenzato model or Global Error Model in Bioconductor
GeneSpring
GeneSpring
updated 18.4 years ago by
Norman Pavelka
▴ 190 • written 18.5 years ago by
Ruppert Valentino
▴ 270
0
votes
1
reply
1.1k
views
RMA and GeneSpring?
Normalization
affy
GeneSpring
Normalization
affy
GeneSpring
updated 20.6 years ago by
Fátima Núñez
▴ 130 • written 20.6 years ago by
Dapeng Cui
▴ 40
0
votes
0
replies
1.1k
views
miRNA array normalization - RMA vs Genespring comparison
miRNA
Normalization
GeneSpring
miRNA
Normalization
GeneSpring
12.3 years ago
Andrea Grilli
▴ 240
0
votes
1
reply
1.1k
views
very small fold change from RMA data
affy
GeneSpring
affy
GeneSpring
updated 20.6 years ago by
Wolfgang Huber
★ 13k • written 20.6 years ago by
Dapeng Cui
▴ 40
0
votes
1
reply
1.1k
views
MLInterfaces
GeneSpring
MLInterfaces
GeneSpring
MLInterfaces
updated 18.2 years ago by
Stephen Henderson
★ 1.0k • written 18.2 years ago by
Qi.Zhang@astrazeneca.com
▴ 60
0
votes
0
replies
1.0k
views
Difference between LIMMA and Genespring
Microarray
Genetics
limma
GeneSpring
Microarray
Genetics
limma
GeneSpring
12.4 years ago
Gordon Smyth
50k
0
votes
1
reply
1.0k
views
How to calculate the values lige GeneSpring from the raw intensities (Agilent)
GeneSpring
GeneSpring
updated 15.9 years ago by
Mark Cowley
▴ 400 • written 15.9 years ago by
olszewski@atlas-biolabs.de
▴ 30
0
votes
2
replies
1.0k
views
RMA results
affy
GeneSpring
affy
GeneSpring
updated 21.3 years ago by
Oliver Hartmann
▴ 70 • written 21.3 years ago by
Duhaime Johanne
▴ 100
0
votes
4
replies
1000
views
R and GeneSpring
GeneSpring
GeneSpring
updated 22.0 years ago by
Anthony Rossini
▴ 530 • written 22.0 years ago by
Jess Mar
▴ 20
0
votes
0
replies
972
views
limma Normalization question
Genetics
Normalization
limma
GeneSpring
limmaGUI
Genetics
Normalization
limma
GeneSpring
18.5 years ago
Cecilia McGregor
▴ 110
0
votes
0
replies
965
views
Limma package for Agilent microarray Image Analysis
limma
GeneSpring
limma
GeneSpring
12.2 years ago
Karthik K N
▴ 200
0
votes
3
replies
958
views
Missing ProbeSets in Affymetrix MoGene 1.0 ST chips
Annotation
cdf
GeneSpring
Annotation
cdf
GeneSpring
updated 15.7 years ago by
James W. MacDonald
65k • written 15.7 years ago by
Mark Cowley
▴ 910
0
votes
0
replies
937
views
JOB: Research Associate at Texas A&M
Clustering
GeneSpring
Clustering
GeneSpring
19.2 years ago
Marina Vannucci
▴ 20
0
votes
1
reply
930
views
questions about Affy package from new user: onemore question
Microarray
Normalization
Cancer
affy
GeneSpring
Microarray
Normalization
Cancer
affy
updated 20.2 years ago by
James W. MacDonald
65k • written 20.2 years ago by
Lizhe Xu
▴ 210
0
votes
0
replies
903
views
Could limma be as good as GeneSpring in normalization?
Microarray
Genetics
limma
GeneSpring
Microarray
Genetics
limma
GeneSpring
19.5 years ago
Elizabeth Brooke-Powell
▴ 160
0
votes
0
replies
901
views
FW: questions about Affy package from new user: onemore question
Microarray
Normalization
Cancer
affy
GeneSpring
Microarray
Normalization
Cancer
affy
20.2 years ago
Lizhe Xu
▴ 210
0
votes
0
replies
887
views
GeneSpring package usage
GeneSpring
GeneSpring
19.8 years ago
marchiem@libero.it
▴ 150
0
votes
0
replies
848
views
agilent shRNA library
Microarray
GeneSpring
Microarray
GeneSpring
13.7 years ago
Giusy Della Gatta
▴ 50
0
votes
0
replies
798
views
What to do about the missing probe sequences for HG_U95A?
Normalization
GO
probe
affy
GeneSpring
Normalization
GO
probe
affy
GeneSpring
19.6 years ago
Thon de Boer
▴ 10
0
votes
1
reply
763
views
maPrintTip confusion
GO
GeneSpring
ASSIGN
GO
GeneSpring
ASSIGN
updated 19.9 years ago by
Jean Yee Hwa Yang
▴ 920 • written 19.9 years ago by
Alison Wise
▴ 10
0
votes
0
replies
751
views
very small fold change from RMA data
affy
GeneSpring
affy
GeneSpring
20.5 years ago
Qiang Li
▴ 10
0
votes
0
replies
739
views
Could limma be as good as GeneSpring in nomalization?
Genetics
limma
GeneSpring
Genetics
limma
GeneSpring
19.5 years ago
donghu@itsa.ucsf.edu
▴ 70
0
votes
1
reply
730
views
questions about Affy package from new user: one more question
Microarray
Normalization
Cancer
GeneSpring
Microarray
Normalization
Cancer
GeneSpring
updated 20.2 years ago by
Adaikalavan Ramasamy
★ 1.8k • written 20.2 years ago by
James W. MacDonald
65k
0
votes
1
reply
717
views
Interface to BASE microarray data
Microarray
Cancer
GeneSpring
Microarray
Cancer
GeneSpring
updated 17.9 years ago by
Henrik Bengtsson
★ 2.4k • written 17.9 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
710
views
affylmGUI - feedback, questions
gcrma
GeneSpring
affylmGUI
gcrma
GeneSpring
affylmGUI
19.3 years ago
SteffenMöller
▴ 30
0
votes
0
replies
698
views
Normalization with common reference
Normalization
Cancer
vsn
GeneSpring
Normalization
Cancer
vsn
GeneSpring
20.0 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
694
views
Error encountered while using RMA
Normalization
GeneSpring
Normalization
GeneSpring
19.6 years ago
Madeleine Gross
▴ 10
0
votes
0
replies
672
views
Getting unmodified Affy-Data via R+ and the Affy package...
GeneSpring
GeneSpring
21.2 years ago
Joern Wessels
▴ 20
0
votes
0
replies
599
views
export toptables into Genespring
limma
GeneSpring
limma
GeneSpring
15.6 years ago
Pemmasani, Kalyani
▴ 10
49 results • Page
1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
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• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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