Showing : genespring • reset
0
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7
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15k
views
How to adjust the Heatmap.2 color key
Microarray GeneSpring Microarray GeneSpring
15.8 years ago Martin Bonke ▴ 40
2
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1
reply
3.5k
views
RNA-seq Differential expression using 3 groups
rnaseq anova deseq2 edger genespring
8.8 years ago BM • 0
0
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1
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3.0k
views
2 way anova in Bioconductor
Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN
updated 12.8 years ago by ▴ 210 • written 12.8 years ago by ▴ 110
0
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2
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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 65k • written 10.2 years ago by ▴ 30
0
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6
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1.9k
views
2 way anova in Bioconductor
GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics GO genefilter
updated 12.9 years ago by ★ 2.0k • written 12.9 years ago by ▴ 110
0
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1
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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 15.6 years ago by 21k • written 15.6 years ago by ▴ 270
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4
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1.7k
views
Should AgiMicroRna and GeneSpring quantile normalisation be the same ?
Normalization GeneSpring microRNA AgiMicroRna Normalization GeneSpring microRNA AgiMicroRna
updated 11.7 years ago by ★ 1.3k • written 11.7 years ago by ▴ 30
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0
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1.5k
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
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2
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1.4k
views
warning messages in gcrma
Microarray Normalization Cancer moe430a moe430b cdf probe affy gcrma siggenes GeneSpring
updated 20.1 years ago by 65k • written 20.2 years ago by ▴ 210
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1
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1.4k
views
Difference between LIMMA and Genespring
limma GeneSpring limma GeneSpring
updated 12.4 years ago by ▴ 230 • written 12.4 years ago by ▴ 10
0
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0
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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
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1.2k
views
limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
18.5 years ago Gordon Smyth 50k
0
votes
4
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1.2k
views
How to cope with arrays hybridized at significantly different time.
GeneSpring GeneSpring
updated 15.2 years ago by ★ 13k • written 15.2 years ago by ▴ 40
0
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3
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1.2k
views
limma - Considering Batch Effect
limma GeneSpring limma GeneSpring
updated 16.8 years ago by 65k • written 16.8 years ago by ▴ 120
0
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2
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1.2k
views
GeneSpring can call R functions?
GO GeneSpring safe GO GeneSpring safe
updated 19.0 years ago by ★ 1.1k • written 19.0 years ago by ▴ 250
0
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0
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1.1k
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
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2
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1.1k
views
Do my Limma results look "normal"?
Microarray Cancer Breast limma GeneSpring Microarray Cancer Breast limma GeneSpring
updated 15.9 years ago by ★ 5.5k • written 15.9 years ago by ★ 1.3k
0
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2
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1.1k
views
Agilent MAGE-ML
RMAGEML GeneSpring PROcess RMAGEML GeneSpring PROcess
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 10
0
votes
2
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1.1k
views
Do my Limma results look "normal"?
Microarray Cancer Breast limma GeneSpring Microarray Cancer Breast limma GeneSpring
updated 15.9 years ago by ★ 1.3k • written 15.9 years ago by 50k
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2
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1.1k
views
som - can it divide the samples into clusters
GeneSpring GeneSpring
19.7 years ago Liu, Xin ▴ 120
0
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3
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1.1k
views
Rocke-Lorenzato model or Global Error Model in Bioconductor
GeneSpring GeneSpring
updated 18.4 years ago by ▴ 190 • written 18.4 years ago by ▴ 270
0
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1
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1.1k
views
RMA and GeneSpring?
Normalization affy GeneSpring Normalization affy GeneSpring
updated 20.6 years ago by ▴ 130 • written 20.6 years ago by ▴ 40
0
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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 ★ 13k • written 20.6 years ago by ▴ 40
0
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1
reply
1.0k
views
MLInterfaces
GeneSpring MLInterfaces GeneSpring MLInterfaces
updated 18.2 years ago by ★ 1.0k • written 18.2 years ago by ▴ 60
0
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0
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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
2
replies
1000
views
RMA results
affy GeneSpring affy GeneSpring
updated 21.3 years ago by ▴ 70 • written 21.3 years ago by ▴ 100
0
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1
reply
999
views
How to calculate the values lige GeneSpring from the raw intensities (Agilent)
GeneSpring GeneSpring
updated 15.9 years ago by ▴ 400 • written 15.9 years ago by ▴ 30
0
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4
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989
views
R and GeneSpring
GeneSpring GeneSpring
updated 22.0 years ago by ▴ 530 • written 22.0 years ago by ▴ 20
0
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0
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965
views
limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
18.5 years ago Cecilia McGregor ▴ 110
0
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0
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960
views
Limma package for Agilent microarray Image Analysis
limma GeneSpring limma GeneSpring
12.2 years ago Karthik K N ▴ 200
0
votes
3
replies
940
views
Missing ProbeSets in Affymetrix MoGene 1.0 ST chips
Annotation cdf GeneSpring Annotation cdf GeneSpring
updated 15.7 years ago by 65k • written 15.7 years ago by ▴ 910
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0
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934
views
JOB: Research Associate at Texas A&M
Clustering GeneSpring Clustering GeneSpring
19.2 years ago Marina Vannucci ▴ 20
0
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1
reply
917
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 65k • written 20.2 years ago by ▴ 210
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votes
0
replies
898
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
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897
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
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881
views
GeneSpring package usage
GeneSpring GeneSpring
19.8 years ago marchiem@libero.it ▴ 150
0
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0
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840
views
agilent shRNA library
Microarray GeneSpring Microarray GeneSpring
13.6 years ago Giusy Della Gatta ▴ 50
0
votes
0
replies
794
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
757
views
maPrintTip confusion
GO GeneSpring ASSIGN GO GeneSpring ASSIGN
updated 19.9 years ago by ▴ 920 • written 19.9 years ago by ▴ 10
0
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0
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749
views
very small fold change from RMA data
affy GeneSpring affy GeneSpring
20.5 years ago Qiang Li ▴ 10
0
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0
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736
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
726
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 ★ 1.8k • written 20.2 years ago by 65k
0
votes
1
reply
712
views
Interface to BASE microarray data
Microarray Cancer GeneSpring Microarray Cancer GeneSpring
updated 17.8 years ago by ★ 2.4k • written 17.8 years ago by ★ 1.9k
0
votes
0
replies
708
views
affylmGUI - feedback, questions
gcrma GeneSpring affylmGUI gcrma GeneSpring affylmGUI
19.2 years ago SteffenMöller ▴ 30
0
votes
0
replies
697
views
Normalization with common reference
Normalization Cancer vsn GeneSpring Normalization Cancer vsn GeneSpring
19.9 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
691
views
Error encountered while using RMA
Normalization GeneSpring Normalization GeneSpring
19.5 years ago Madeleine Gross ▴ 10
0
votes
0
replies
666
views
Getting unmodified Affy-Data via R+ and the Affy package...
GeneSpring GeneSpring
21.1 years ago Joern Wessels ▴ 20
0
votes
0
replies
597
views
export toptables into Genespring
limma GeneSpring limma GeneSpring
15.5 years ago Pemmasani, Kalyani ▴ 10
49 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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