Showing : genespring • reset
2
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RNA-seq Differential expression using 3 groups
rnaseq anova deseq2 edger genespring
8.8 years ago BM • 0
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2
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2.2k
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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
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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 11.8 years ago by ★ 1.3k • written 11.8 years ago by ▴ 30
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965
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Limma package for Agilent microarray Image Analysis
limma GeneSpring limma GeneSpring
12.2 years ago Karthik K N ▴ 200
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1.1k
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miRNA array normalization - RMA vs Genespring comparison
miRNA Normalization GeneSpring miRNA Normalization GeneSpring
12.3 years ago Andrea Grilli ▴ 240
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0
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1.0k
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Difference between LIMMA and Genespring
Microarray Genetics limma GeneSpring Microarray Genetics limma GeneSpring
12.4 years ago Gordon Smyth 50k
0
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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
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3.0k
views
2 way anova in Bioconductor
Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN
updated 12.9 years ago by ▴ 210 • written 12.9 years ago by ▴ 110
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6
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2.0k
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
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848
views
agilent shRNA library
Microarray GeneSpring Microarray GeneSpring
13.7 years ago Giusy Della Gatta ▴ 50
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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
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599
views
export toptables into Genespring
limma GeneSpring limma GeneSpring
15.6 years ago Pemmasani, Kalyani ▴ 10
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 15.7 years ago by 21k • written 15.7 years ago by ▴ 270
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3
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958
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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2
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1.2k
views
Agilent MAGE-ML
RMAGEML GeneSpring PROcess RMAGEML GeneSpring PROcess
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 10
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7
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16k
views
How to adjust the Heatmap.2 color key
Microarray GeneSpring Microarray GeneSpring
15.9 years ago Martin Bonke ▴ 40
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0
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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
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1
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1.0k
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
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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 16.0 years ago by ★ 1.3k • written 16.0 years ago by 50k
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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 16.0 years ago by ★ 5.5k • written 16.0 years ago by ★ 1.3k
0
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3
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1.2k
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limma - Considering Batch Effect
limma GeneSpring limma GeneSpring
updated 16.8 years ago by 65k • written 16.8 years ago by ▴ 120
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1
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717
views
Interface to BASE microarray data
Microarray Cancer GeneSpring Microarray Cancer GeneSpring
updated 17.9 years ago by ★ 2.4k • written 17.9 years ago by ★ 1.9k
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1
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1.1k
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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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 18.5 years ago by ▴ 270
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2
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1.2k
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limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
18.5 years ago Gordon Smyth 50k
0
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0
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972
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limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
18.5 years ago Cecilia McGregor ▴ 110
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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
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937
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JOB: Research Associate at Texas A&M
Clustering GeneSpring Clustering GeneSpring
19.2 years ago Marina Vannucci ▴ 20
0
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710
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affylmGUI - feedback, questions
gcrma GeneSpring affylmGUI gcrma GeneSpring affylmGUI
19.3 years ago SteffenMöller ▴ 30
0
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0
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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
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903
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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
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694
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Error encountered while using RMA
Normalization GeneSpring Normalization GeneSpring
19.6 years ago Madeleine Gross ▴ 10
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0
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798
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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
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1.1k
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som - can it divide the samples into clusters
GeneSpring GeneSpring
19.8 years ago Liu, Xin ▴ 120
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0
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887
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GeneSpring package usage
GeneSpring GeneSpring
19.8 years ago marchiem@libero.it ▴ 150
0
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1
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763
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maPrintTip confusion
GO GeneSpring ASSIGN GO GeneSpring ASSIGN
updated 19.9 years ago by ▴ 920 • written 19.9 years ago by ▴ 10
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Normalization with common reference
Normalization Cancer vsn GeneSpring Normalization Cancer vsn GeneSpring
20.0 years ago Wolfgang Huber ★ 13k
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1.2k
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median polish vs mas/PLIER info
Microarray Normalization Cancer probe affy GeneSpring PROcess plier Microarray Cancer
20.0 years ago Anthony Bosco ▴ 500
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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
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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 20.2 years ago by 65k • written 20.2 years ago by ▴ 210
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901
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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
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1
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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 65k • written 20.2 years ago by ▴ 210
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1
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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 ★ 1.8k • written 20.2 years ago by 65k
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751
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very small fold change from RMA data
affy GeneSpring affy GeneSpring
20.5 years ago Qiang Li ▴ 10
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1
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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
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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
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0
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672
views
Getting unmodified Affy-Data via R+ and the Affy package...
GeneSpring GeneSpring
21.2 years ago Joern Wessels ▴ 20
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2
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1.0k
views
RMA results
affy GeneSpring affy GeneSpring
updated 21.3 years ago by ▴ 70 • written 21.3 years ago by ▴ 100
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4
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1000
views
R and GeneSpring
GeneSpring GeneSpring
updated 22.0 years ago by ▴ 530 • written 22.0 years ago by ▴ 20
49 results • Page 1 of 1
Recent ...
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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: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 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?
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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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