Showing : genespring • reset
2
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RNA-seq Differential expression using 3 groups
rnaseq anova deseq2 edger genespring
10.4 years ago BM • 0
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2
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2.6k
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First time use of limma for two-color agilent array analysis
qPCR limma GeneSpring qPCR limma GeneSpring
updated 11.8 years ago by 68k • written 11.8 years ago by ▴ 30
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4
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2.3k
views
Should AgiMicroRna and GeneSpring quantile normalisation be the same ?
Normalization GeneSpring microRNA AgiMicroRna Normalization GeneSpring microRNA AgiMicroRna
updated 13.3 years ago by ★ 1.3k • written 13.3 years ago by ▴ 30
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Limma package for Agilent microarray Image Analysis
limma GeneSpring limma GeneSpring
13.8 years ago Karthik K N ▴ 200
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miRNA array normalization - RMA vs Genespring comparison
miRNA Normalization GeneSpring miRNA Normalization GeneSpring
13.9 years ago Andrea Grilli ▴ 240
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1.3k
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Difference between LIMMA and Genespring
Microarray Genetics limma GeneSpring Microarray Genetics limma GeneSpring
14.0 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 14.0 years ago by ▴ 230 • written 14.0 years ago by ▴ 10
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3.4k
views
2 way anova in Bioconductor
Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN
updated 14.4 years ago by ▴ 210 • written 14.4 years ago by ▴ 110
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6
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2.6k
views
2 way anova in Bioconductor
GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics GO genefilter
updated 14.4 years ago by ★ 2.0k • written 14.4 years ago by ▴ 110
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1.1k
views
agilent shRNA library
Microarray GeneSpring Microarray GeneSpring
15.2 years ago Giusy Della Gatta ▴ 50
0
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4
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1.6k
views
How to cope with arrays hybridized at significantly different time.
GeneSpring GeneSpring
updated 16.7 years ago by ★ 13k • written 16.7 years ago by ▴ 40
0
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799
views
export toptables into Genespring
limma GeneSpring limma GeneSpring
17.1 years ago Pemmasani, Kalyani ▴ 10
0
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1
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2.4k
views
what is the best baseline transformation method before clustering
GO Clustering probe affy gcrma GeneSpring GO Clustering probe affy gcrma GeneSpring
updated 17.2 years ago by 21k • written 17.2 years ago by ▴ 270
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3
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1.3k
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Missing ProbeSets in Affymetrix MoGene 1.0 ST chips
Annotation cdf GeneSpring Annotation cdf GeneSpring
updated 17.3 years ago by 68k • written 17.3 years ago by ▴ 910
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2
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1.5k
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Agilent MAGE-ML
RMAGEML GeneSpring PROcess RMAGEML GeneSpring PROcess
updated 17.3 years ago by 25k • written 17.3 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
17.4 years ago Martin Bonke ▴ 40
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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
17.5 years ago Mark Cowley ▴ 400
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1
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1.4k
views
How to calculate the values lige GeneSpring from the raw intensities (Agilent)
GeneSpring GeneSpring
updated 17.5 years ago by ▴ 400 • written 17.5 years ago by ▴ 30
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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 17.5 years ago by ★ 1.3k • written 17.5 years ago by 53k
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2
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Do my Limma results look "normal"?
Microarray Cancer Breast limma GeneSpring Microarray Cancer Breast limma GeneSpring
updated 17.5 years ago by ★ 5.5k • written 17.5 years ago by ★ 1.3k
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3
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1.6k
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limma - Considering Batch Effect
limma GeneSpring limma GeneSpring
updated 18.3 years ago by 68k • written 18.3 years ago by ▴ 120
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1
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938
views
Interface to BASE microarray data
Microarray Cancer GeneSpring Microarray Cancer GeneSpring
updated 19.4 years ago by ★ 2.4k • written 19.4 years ago by ★ 1.9k
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1
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1.3k
views
MLInterfaces
GeneSpring MLInterfaces GeneSpring MLInterfaces
updated 19.8 years ago by ★ 1.0k • written 19.8 years ago by ▴ 60
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3
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1.5k
views
Rocke-Lorenzato model or Global Error Model in Bioconductor
GeneSpring GeneSpring
updated 20.0 years ago by ▴ 190 • written 20.0 years ago by ▴ 270
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2
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1.6k
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limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
20.0 years ago Gordon Smyth 53k
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1.2k
views
limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
20.1 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 20.6 years ago by ★ 1.1k • written 20.6 years ago by ▴ 250
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1.1k
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JOB: Research Associate at Texas A&M
Clustering GeneSpring Clustering GeneSpring
20.7 years ago Marina Vannucci ▴ 20
0
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0
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901
views
affylmGUI - feedback, questions
gcrma GeneSpring affylmGUI gcrma GeneSpring affylmGUI
20.8 years ago SteffenMöller ▴ 30
0
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0
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930
views
Could limma be as good as GeneSpring in nomalization?
Genetics limma GeneSpring Genetics limma GeneSpring
21.0 years ago donghu@itsa.ucsf.edu ▴ 70
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1.1k
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Could limma be as good as GeneSpring in normalization?
Microarray Genetics limma GeneSpring Microarray Genetics limma GeneSpring
21.0 years ago Elizabeth Brooke-Powell ▴ 160
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880
views
Error encountered while using RMA
Normalization GeneSpring Normalization GeneSpring
21.1 years ago Madeleine Gross ▴ 10
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996
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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
21.2 years ago Thon de Boer ▴ 10
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2
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1.5k
views
som - can it divide the samples into clusters
GeneSpring GeneSpring
21.3 years ago Liu, Xin ▴ 120
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1.1k
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GeneSpring package usage
GeneSpring GeneSpring
21.3 years ago marchiem@libero.it ▴ 150
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1
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1.0k
views
maPrintTip confusion
GO GeneSpring ASSIGN GO GeneSpring ASSIGN
updated 21.5 years ago by ▴ 920 • written 21.5 years ago by ▴ 10
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Normalization with common reference
Normalization Cancer vsn GeneSpring Normalization Cancer vsn GeneSpring
21.5 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
21.6 years ago Anthony Bosco ▴ 500
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0
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1.6k
views
MAS vs gcrma, rma and Li-Wong method in Affy package for TC study
Normalization Clustering affy gcrma GeneSpring Normalization Clustering affy gcrma
21.7 years ago Lizhe Xu ▴ 210
0
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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 21.7 years ago by 68k • written 21.7 years ago by ▴ 210
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1.2k
views
questions about Affy package from new user: onemore question
Microarray Normalization Cancer affy GeneSpring Microarray Normalization Cancer affy
updated 21.7 years ago by 68k • written 21.7 years ago by ▴ 210
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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
21.7 years ago Lizhe Xu ▴ 210
0
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1
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959
views
questions about Affy package from new user: one more question
Microarray Normalization Cancer GeneSpring Microarray Normalization Cancer GeneSpring
updated 21.7 years ago by ★ 1.8k • written 21.7 years ago by 68k
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949
views
very small fold change from RMA data
affy GeneSpring affy GeneSpring
22.1 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 22.2 years ago by ★ 13k • written 22.2 years ago by ▴ 40
0
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1
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1.4k
views
RMA and GeneSpring?
Normalization affy GeneSpring Normalization affy GeneSpring
updated 22.2 years ago by ▴ 130 • written 22.2 years ago by ▴ 40
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0
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880
views
Getting unmodified Affy-Data via R+ and the Affy package...
GeneSpring GeneSpring
22.7 years ago Joern Wessels ▴ 20
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2
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1.4k
views
RMA results
affy GeneSpring affy GeneSpring
updated 22.9 years ago by ▴ 70 • written 22.9 years ago by ▴ 100
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4
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1.4k
views
R and GeneSpring
GeneSpring GeneSpring
updated 23.6 years ago by ▴ 530 • written 23.6 years ago by ▴ 20
49 results • Page 1 of 1
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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