Showing : genespring • reset
2
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4.0k
views
RNA-seq Differential expression using 3 groups
rnaseq anova deseq2 edger genespring
10.2 years ago BM • 0
0
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2
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2.5k
views
First time use of limma for two-color agilent array analysis
qPCR limma GeneSpring qPCR limma GeneSpring
updated 11.6 years ago by 68k • written 11.6 years ago by ▴ 30
0
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4
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2.2k
views
Should AgiMicroRna and GeneSpring quantile normalisation be the same ?
Normalization GeneSpring microRNA AgiMicroRna Normalization GeneSpring microRNA AgiMicroRna
updated 13.1 years ago by ★ 1.3k • written 13.1 years ago by ▴ 30
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1.1k
views
Limma package for Agilent microarray Image Analysis
limma GeneSpring limma GeneSpring
13.6 years ago Karthik K N ▴ 200
0
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1.3k
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miRNA array normalization - RMA vs Genespring comparison
miRNA Normalization GeneSpring miRNA Normalization GeneSpring
13.7 years ago Andrea Grilli ▴ 240
0
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0
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1.2k
views
Difference between LIMMA and Genespring
Microarray Genetics limma GeneSpring Microarray Genetics limma GeneSpring
13.8 years ago Gordon Smyth 53k
0
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1
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1.7k
views
Difference between LIMMA and Genespring
limma GeneSpring limma GeneSpring
updated 13.8 years ago by ▴ 230 • written 13.8 years ago by ▴ 10
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1
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3.4k
views
2 way anova in Bioconductor
Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN
updated 14.2 years ago by ▴ 210 • written 14.2 years ago by ▴ 110
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6
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2.5k
views
2 way anova in Bioconductor
GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics GO genefilter
updated 14.3 years ago by ★ 2.0k • written 14.3 years ago by ▴ 110
0
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1.1k
views
agilent shRNA library
Microarray GeneSpring Microarray GeneSpring
15.0 years ago Giusy Della Gatta ▴ 50
0
votes
4
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1.6k
views
How to cope with arrays hybridized at significantly different time.
GeneSpring GeneSpring
updated 16.6 years ago by ★ 13k • written 16.6 years ago by ▴ 40
0
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760
views
export toptables into Genespring
limma GeneSpring limma GeneSpring
16.9 years ago Pemmasani, Kalyani ▴ 10
0
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1
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2.3k
views
what is the best baseline transformation method before clustering
GO Clustering probe affy gcrma GeneSpring GO Clustering probe affy gcrma GeneSpring
updated 17.0 years ago by 21k • written 17.0 years ago by ▴ 270
0
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3
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1.3k
views
Missing ProbeSets in Affymetrix MoGene 1.0 ST chips
Annotation cdf GeneSpring Annotation cdf GeneSpring
updated 17.1 years ago by 68k • written 17.1 years ago by ▴ 910
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2
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1.4k
views
Agilent MAGE-ML
RMAGEML GeneSpring PROcess RMAGEML GeneSpring PROcess
updated 17.1 years ago by 25k • written 17.1 years ago by ▴ 10
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7
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17k
views
How to adjust the Heatmap.2 color key
Microarray GeneSpring Microarray GeneSpring
17.2 years ago Martin Bonke ▴ 40
0
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0
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1.9k
views
Cutoff to use for IQR filtering in genefilter
genefilter affy limma GeneSpring affylmGUI GLAD SIM genefilter affy limma GeneSpring
17.3 years ago Mark Cowley ▴ 400
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1
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1.3k
views
How to calculate the values lige GeneSpring from the raw intensities (Agilent)
GeneSpring GeneSpring
updated 17.3 years ago by ▴ 400 • written 17.3 years ago by ▴ 30
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2
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1.4k
views
Do my Limma results look "normal"?
Microarray Cancer Breast limma GeneSpring Microarray Cancer Breast limma GeneSpring
updated 17.3 years ago by ★ 1.3k • written 17.3 years ago by 53k
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2
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1.5k
views
Do my Limma results look "normal"?
Microarray Cancer Breast limma GeneSpring Microarray Cancer Breast limma GeneSpring
updated 17.3 years ago by ★ 5.5k • written 17.3 years ago by ★ 1.3k
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3
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1.5k
views
limma - Considering Batch Effect
limma GeneSpring limma GeneSpring
updated 18.1 years ago by 68k • written 18.1 years ago by ▴ 120
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1
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895
views
Interface to BASE microarray data
Microarray Cancer GeneSpring Microarray Cancer GeneSpring
updated 19.2 years ago by ★ 2.4k • written 19.2 years ago by ★ 1.9k
0
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1
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1.3k
views
MLInterfaces
GeneSpring MLInterfaces GeneSpring MLInterfaces
updated 19.6 years ago by ★ 1.0k • written 19.6 years ago by ▴ 60
0
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3
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1.4k
views
Rocke-Lorenzato model or Global Error Model in Bioconductor
GeneSpring GeneSpring
updated 19.8 years ago by ▴ 190 • written 19.8 years ago by ▴ 270
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2
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1.6k
views
limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
19.9 years ago Gordon Smyth 53k
0
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0
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1.2k
views
limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
19.9 years ago Cecilia McGregor ▴ 110
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2
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1.6k
views
GeneSpring can call R functions?
GO GeneSpring safe GO GeneSpring safe
updated 20.4 years ago by ★ 1.1k • written 20.4 years ago by ▴ 250
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JOB: Research Associate at Texas A&M
Clustering GeneSpring Clustering GeneSpring
20.6 years ago Marina Vannucci ▴ 20
0
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0
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868
views
affylmGUI - feedback, questions
gcrma GeneSpring affylmGUI gcrma GeneSpring affylmGUI
20.6 years ago SteffenMöller ▴ 30
0
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0
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899
views
Could limma be as good as GeneSpring in nomalization?
Genetics limma GeneSpring Genetics limma GeneSpring
20.8 years ago donghu@itsa.ucsf.edu ▴ 70
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1.1k
views
Could limma be as good as GeneSpring in normalization?
Microarray Genetics limma GeneSpring Microarray Genetics limma GeneSpring
20.8 years ago Elizabeth Brooke-Powell ▴ 160
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858
views
Error encountered while using RMA
Normalization GeneSpring Normalization GeneSpring
20.9 years ago Madeleine Gross ▴ 10
0
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0
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960
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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
21.0 years ago Thon de Boer ▴ 10
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2
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1.4k
views
som - can it divide the samples into clusters
GeneSpring GeneSpring
21.1 years ago Liu, Xin ▴ 120
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0
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1.1k
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GeneSpring package usage
GeneSpring GeneSpring
21.2 years ago marchiem@libero.it ▴ 150
0
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1
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973
views
maPrintTip confusion
GO GeneSpring ASSIGN GO GeneSpring ASSIGN
updated 21.3 years ago by ▴ 920 • written 21.3 years ago by ▴ 10
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863
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Normalization with common reference
Normalization Cancer vsn GeneSpring Normalization Cancer vsn GeneSpring
21.3 years ago Wolfgang Huber ★ 13k
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1.4k
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median polish vs mas/PLIER info
Microarray Normalization Cancer probe affy GeneSpring PROcess plier Microarray Cancer
21.4 years ago Anthony Bosco ▴ 500
0
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0
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1.5k
views
MAS vs gcrma, rma and Li-Wong method in Affy package for TC study
Normalization Clustering affy gcrma GeneSpring Normalization Clustering affy gcrma
21.5 years ago Lizhe Xu ▴ 210
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2
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1.7k
views
warning messages in gcrma
Microarray Normalization Cancer moe430a moe430b cdf probe affy gcrma siggenes GeneSpring
updated 21.5 years ago by 68k • written 21.5 years ago by ▴ 210
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1
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1.1k
views
questions about Affy package from new user: onemore question
Microarray Normalization Cancer affy GeneSpring Microarray Normalization Cancer affy
updated 21.5 years ago by 68k • written 21.5 years ago by ▴ 210
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0
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1.1k
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FW: questions about Affy package from new user: onemore question
Microarray Normalization Cancer affy GeneSpring Microarray Normalization Cancer affy
21.5 years ago Lizhe Xu ▴ 210
0
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1
reply
926
views
questions about Affy package from new user: one more question
Microarray Normalization Cancer GeneSpring Microarray Normalization Cancer GeneSpring
updated 21.5 years ago by ★ 1.8k • written 21.5 years ago by 68k
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907
views
very small fold change from RMA data
affy GeneSpring affy GeneSpring
21.9 years ago Qiang Li ▴ 10
0
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1
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1.3k
views
very small fold change from RMA data
affy GeneSpring affy GeneSpring
updated 22.0 years ago by ★ 13k • written 22.0 years ago by ▴ 40
0
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1
reply
1.3k
views
RMA and GeneSpring?
Normalization affy GeneSpring Normalization affy GeneSpring
updated 22.0 years ago by ▴ 130 • written 22.0 years ago by ▴ 40
0
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0
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841
views
Getting unmodified Affy-Data via R+ and the Affy package...
GeneSpring GeneSpring
22.5 years ago Joern Wessels ▴ 20
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2
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1.3k
views
RMA results
affy GeneSpring affy GeneSpring
updated 22.7 years ago by ▴ 70 • written 22.7 years ago by ▴ 100
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4
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1.4k
views
R and GeneSpring
GeneSpring GeneSpring
updated 23.4 years ago by ▴ 530 • written 23.4 years ago by ▴ 20
49 results • Page 1 of 1
Recent ...
Replies
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by ReinholdGaylord99 • 0
Thank you so much! https://www.nature.com/articles/s41467-021-25960-2/ [geometry dash lite](https://geometrydashlite.online)
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
I'm not sure that I understand. You have a dataset that, even after pseudo-bulking, still has 6000 samples? That is surprising. Retaining …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Hello again @gordonsmyth, I've now applied the analysis using a more detailed annotation of cell types/clusters, which includes about 100 …
Answer: Sharing a collection of datasets in ExperimentHub by shepherl 4.2k
107 packages would be a lot! It is certainly possible (and recommended) to implement one package that utilizes ExperimentHub for controlli…
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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