Showing : genespring • reset
2
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RNA-seq Differential expression using 3 groups
rnaseq anova deseq2 edger genespring
8.9 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 10.3 years ago by 66k • written 10.3 years ago by ▴ 30
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4
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1.8k
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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 11.9 years ago by ▴ 30
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974
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Limma package for Agilent microarray Image Analysis
limma GeneSpring limma GeneSpring
12.3 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
12.4 years ago Andrea Grilli ▴ 240
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1.0k
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Difference between LIMMA and Genespring
Microarray Genetics limma GeneSpring Microarray Genetics limma GeneSpring
12.5 years ago Gordon Smyth 51k
0
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1
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1.4k
views
Difference between LIMMA and Genespring
limma GeneSpring limma GeneSpring
updated 12.5 years ago by ▴ 230 • written 12.5 years ago by ▴ 10
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3.0k
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2 way anova in Bioconductor
Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN
updated 13.0 years ago by ▴ 210 • written 13.0 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 13.0 years ago by ★ 2.0k • written 13.0 years ago by ▴ 110
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859
views
agilent shRNA library
Microarray GeneSpring Microarray GeneSpring
13.8 years ago Giusy Della Gatta ▴ 50
0
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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 15.3 years ago by ★ 13k • written 15.3 years ago by ▴ 40
0
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608
views
export toptables into Genespring
limma GeneSpring limma GeneSpring
15.7 years ago Pemmasani, Kalyani ▴ 10
0
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1
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2.0k
views
what is the best baseline transformation method before clustering
GO Clustering probe affy gcrma GeneSpring GO Clustering probe affy gcrma GeneSpring
updated 15.8 years ago by 21k • written 15.8 years ago by ▴ 270
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3
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996
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Missing ProbeSets in Affymetrix MoGene 1.0 ST chips
Annotation cdf GeneSpring Annotation cdf GeneSpring
updated 15.8 years ago by 66k • written 15.8 years ago by ▴ 910
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2
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1.2k
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Agilent MAGE-ML
RMAGEML GeneSpring PROcess RMAGEML GeneSpring PROcess
updated 15.8 years ago by 25k • written 15.9 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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1.6k
views
Cutoff to use for IQR filtering in genefilter
genefilter affy limma GeneSpring affylmGUI GLAD SIM genefilter affy limma GeneSpring
16.0 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 16.0 years ago by ▴ 400 • written 16.0 years ago by ▴ 30
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2
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1.2k
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 51k
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2
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1.2k
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
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3
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1.3k
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limma - Considering Batch Effect
limma GeneSpring limma GeneSpring
updated 16.9 years ago by 66k • written 16.9 years ago by ▴ 120
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1
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723
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 18.3 years ago by ★ 1.0k • written 18.3 years ago by ▴ 60
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3
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1.1k
views
Rocke-Lorenzato model or Global Error Model in Bioconductor
GeneSpring GeneSpring
updated 18.5 years ago by ▴ 190 • written 18.5 years ago by ▴ 270
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2
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1.3k
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limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
18.6 years ago Gordon Smyth 51k
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0
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984
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limma Normalization question
Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring
18.6 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 19.1 years ago by ★ 1.1k • written 19.1 years ago by ▴ 250
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JOB: Research Associate at Texas A&M
Clustering GeneSpring Clustering GeneSpring
19.3 years ago Marina Vannucci ▴ 20
0
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0
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721
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affylmGUI - feedback, questions
gcrma GeneSpring affylmGUI gcrma GeneSpring affylmGUI
19.4 years ago SteffenMöller ▴ 30
0
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0
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747
views
Could limma be as good as GeneSpring in nomalization?
Genetics limma GeneSpring Genetics limma GeneSpring
19.6 years ago donghu@itsa.ucsf.edu ▴ 70
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913
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Could limma be as good as GeneSpring in normalization?
Microarray Genetics limma GeneSpring Microarray Genetics limma GeneSpring
19.6 years ago Elizabeth Brooke-Powell ▴ 160
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702
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Error encountered while using RMA
Normalization GeneSpring Normalization GeneSpring
19.7 years ago Madeleine Gross ▴ 10
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0
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806
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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
19.7 years ago Thon de Boer ▴ 10
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2
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1.1k
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som - can it divide the samples into clusters
GeneSpring GeneSpring
19.9 years ago Liu, Xin ▴ 120
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0
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896
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GeneSpring package usage
GeneSpring GeneSpring
19.9 years ago marchiem@libero.it ▴ 150
0
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1
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774
views
maPrintTip confusion
GO GeneSpring ASSIGN GO GeneSpring ASSIGN
updated 20.0 years ago by ▴ 920 • written 20.0 years ago by ▴ 10
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Normalization with common reference
Normalization Cancer vsn GeneSpring Normalization Cancer vsn GeneSpring
20.1 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
20.1 years ago Anthony Bosco ▴ 500
0
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0
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1.3k
views
MAS vs gcrma, rma and Li-Wong method in Affy package for TC study
Normalization Clustering affy gcrma GeneSpring Normalization Clustering affy gcrma
20.2 years ago Lizhe Xu ▴ 210
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 20.3 years ago by 66k • written 20.3 years ago by ▴ 210
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1
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957
views
questions about Affy package from new user: onemore question
Microarray Normalization Cancer affy GeneSpring Microarray Normalization Cancer affy
updated 20.3 years ago by 66k • written 20.3 years ago by ▴ 210
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0
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907
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FW: questions about Affy package from new user: onemore question
Microarray Normalization Cancer affy GeneSpring Microarray Normalization Cancer affy
20.3 years ago Lizhe Xu ▴ 210
0
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1
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735
views
questions about Affy package from new user: one more question
Microarray Normalization Cancer GeneSpring Microarray Normalization Cancer GeneSpring
updated 20.3 years ago by ★ 1.8k • written 20.3 years ago by 66k
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0
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762
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very small fold change from RMA data
affy GeneSpring affy GeneSpring
20.6 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 20.7 years ago by ★ 13k • written 20.7 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 20.7 years ago by ▴ 130 • written 20.7 years ago by ▴ 40
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0
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682
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 21.4 years ago by ▴ 70 • written 21.4 years ago by ▴ 100
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4
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1.0k
views
R and GeneSpring
GeneSpring GeneSpring
updated 22.1 years ago by ▴ 530 • written 22.1 years ago by ▴ 20
49 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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Popular Question to Frederico Moraes Ferreira ▴ 100
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