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Creating a model matrix for three age groups using two-colour arrays
Microarray BRAIN Microarray BRAIN
updated 3.9 years ago by 52k • written 16.1 years ago by ▴ 10
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Job: Data science research assistant position at Johns Hopkins
RNAseq R Next-Gen Sequencing Imaging Brain Job
5.7 years ago hjaarop1 • 0
0
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1
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1.3k
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CAGEr - How to change plot axis range in CAGEr
BRAIN CAGEr BRAIN CAGEr
updated 6.7 years ago by ▴ 180 • written 10.4 years ago by ▴ 10
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2
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2.1k
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How to proceed with different degradation levels of RNA-seq samples?
degradation RNA-seq variability differential expression brain
updated 7.7 years ago by ★ 28k • written 7.8 years ago by ▴ 90
0
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9
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3.1k
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frma and alternative CDFs
GO cdf frma BRAIN GO cdf frma BRAIN
updated 10.4 years ago by ▴ 830 • written 10.4 years ago by ★ 13k
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Job reminder: Open position for a Core Bioinformatician in Lund, Sweden
Microarray BRAIN Microarray BRAIN
11.5 years ago _Bio - Informatics ▴ 20
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1.3k
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Open position for a Core Bioinformatician in Lund, Sweden
Microarray BRAIN Microarray BRAIN
11.5 years ago _Bio - Informatics ▴ 20
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1.1k
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Error in example from biomaRt vignette
biomaRt BRAIN biomaRt BRAIN
11.7 years ago Steffen Durinck ▴ 90
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2.1k
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Tukey\'s HSD after ANOVA
GO BRAIN GO BRAIN
11.7 years ago Guest User ★ 13k
0
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0
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850
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Differentially regulated genes
BRAIN BRAIN
11.9 years ago Ali Mohammadian ▴ 290
0
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1
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1.4k
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log2 and rowMeans a problem?
BRAIN BRAIN
updated 12.1 years ago by ★ 4.3k • written 12.1 years ago by ▴ 20
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3
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1.3k
views
edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
updated 12.5 years ago by 25k • written 12.5 years ago by 52k
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1.3k
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edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
12.5 years ago alessandro.guffanti@genomnia.com ▴ 330
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1
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1.4k
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Three tenure track assistant professorship openings at Inst. Behavioral Genetics, University of Colorado Boulder
Genetics BRAIN Genetics BRAIN
12.8 years ago Matthew Keller ▴ 100
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1.0k
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What is the difference of layout between genepix scanner & agilent scanner
limma BRAIN limma BRAIN
13.2 years ago 이선재 ▴ 30
0
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1
reply
1.3k
views
[question] integration of microarray data from different sources in limma package
Microarray limma BRAIN Microarray limma BRAIN
updated 13.3 years ago by ▴ 340 • written 13.3 years ago by ▴ 30
0
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1
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1.1k
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[question] integration of microarray data from different sources in limma package
Microarray limma BRAIN Microarray limma BRAIN
updated 13.3 years ago by ▴ 150 • written 13.3 years ago by ▴ 30
0
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7
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1.8k
views
EBS volumes with the Bioconductor AMI: how to change default behaviour
PROcess BRAIN PROcess BRAIN
13.4 years ago Dan Tenenbaum ★ 8.2k
0
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2
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1.4k
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EBS volumes with the Bioconductor AMI: how to change default behaviour
BRAIN BRAIN
13.4 years ago Quin Wills ▴ 80
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1
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3.2k
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2 way anova in Bioconductor
Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN
updated 13.5 years ago by ▴ 210 • written 13.5 years ago by ▴ 110
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0
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907
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How to: design matrices for multi organism parts experiment
Organism BRAIN Organism BRAIN
13.6 years ago Hans ▴ 10
0
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3
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1.5k
views
How to filter a list of SNPs?
BRAIN BRAIN
updated 13.7 years ago by ★ 13k • written 13.7 years ago by ▴ 450
0
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1
reply
1.8k
views
Modeling of methylation status using lumi
Microarray lumi BRAIN Microarray lumi BRAIN
updated 13.8 years ago by ▴ 80 • written 13.8 years ago by ▴ 620
0
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0
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1.1k
views
Modeling of methylation status using lumi
Microarray lumi BRAIN Microarray lumi BRAIN
14.1 years ago Pan Du ★ 1.2k
0
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3
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1.4k
views
Microarray experiments with Drosophilas (miniscule amounts of RNA, cheap organisms)
Microarray BRAIN Microarray BRAIN
updated 14.2 years ago by ▴ 10 • written 14.2 years ago by ▴ 40
0
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0
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943
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How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
15.9 years ago Gordon Smyth 52k
0
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0
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881
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
15.9 years ago Dmitriy Verkhoturov ▴ 10
0
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3
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1.4k
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problems with paired design in limma
Microarray BRAIN Microarray BRAIN
16.1 years ago Michael Walter ▴ 160
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0
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920
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Creating a model matrix for three age groups using two-colour arrays
Microarray limma BRAIN Microarray limma BRAIN
16.1 years ago Gordon Smyth 52k
0
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4
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2.0k
views
allen brain atlas
Genetics Annotation BRAIN Genetics Annotation BRAIN
updated 16.4 years ago by 25k • written 16.4 years ago by ▴ 60
0
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0
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884
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MAQC samples on Affymarix Exon array
BRAIN BRAIN
16.4 years ago Weiyin Zhou ▴ 20
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5
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1.5k
views
P-values for tissue specific genes
BRAIN BRAIN
16.5 years ago Pascal Gellert ▴ 30
0
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1
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1.2k
views
new lumi and miRNA array data
Microarray Normalization lumi BRAIN Microarray Normalization lumi BRAIN
updated 16.7 years ago by ★ 13k • written 16.7 years ago by ▴ 830
0
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2
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1.7k
views
new topGO results using GO.db very different from old ones using GO
GO annotate topGO BRAIN GO annotate topGO BRAIN
updated 16.7 years ago by ▴ 400 • written 16.7 years ago by ▴ 730
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0
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946
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The above Feelgood Formula enshrines the common philosophy that the better you treat people, the better they will work.
Pathways PROcess BRAIN Pathways PROcess BRAIN
17.5 years ago Neddy ▴ 10
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0
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1.2k
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Undergraduate Student Project Summer 2007, at EBI: the synapse and the brain
Pathways BRAIN Pathways BRAIN
17.9 years ago Wolfgang Huber ★ 13k
0
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0
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955
views
read.maimages broken (limma 2.9.10)?
limma BRAIN limma BRAIN
17.9 years ago Gordon Smyth 52k
0
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0
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874
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read.maimages broken (limma 2.9.10)?
BRAIN BRAIN
17.9 years ago Koen Bossers ▴ 10
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0
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1.3k
views
microarray analysis of a dose response * strain experiment
Microarray affy limma maSigPro DOSE BRAIN Microarray affy limma maSigPro DOSE BRAIN
18.2 years ago Naomi Altman ★ 6.0k
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4
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1.7k
views
microarray analysis of a dose response * strain experiment
affy DOSE BRAIN affy DOSE BRAIN
updated 18.2 years ago by 21k • written 18.2 years ago by ▴ 890
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0
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1.1k
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4 replicates, of 3 tissues- one good hyb (2xreps), one bad hyb (2xreps). Best way forward?
qPCR affy affydata vsn limma gcrma matchprobes affyPLM affyio BRAIN qPCR affy affydata
18.3 years ago k. brand ▴ 420
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1
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1.2k
views
GCRMA
Microarray Preprocessing gcrma BRAIN Microarray Preprocessing gcrma BRAIN
updated 19.0 years ago by ★ 2.0k • written 19.0 years ago by ▴ 20
0
votes
3
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1.6k
views
LIMMA lmscFit: difference between linear models
BRAIN BRAIN
19.3 years ago Koen Bossers ▴ 20
0
votes
3
replies
1.2k
views
limma design matrix
affy BRAIN affy BRAIN
updated 20.0 years ago by ▴ 720 • written 20.0 years ago by ▴ 250
0
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1
reply
1.5k
views
Cluster analysis distance measuer
Microarray Annotation Normalization Clustering Cancer affy limma AnnBuilder BRAIN Cancer
updated 20.2 years ago by ▴ 110 • written 20.2 years ago by ▴ 250
0
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0
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1.0k
views
help with limma contrast matrix
BRAIN BRAIN
20.2 years ago Kimpel, Mark W ▴ 890
0
votes
3
replies
1.6k
views
human tissue specific genes
BRAIN BRAIN
updated 20.4 years ago by 21k • written 20.4 years ago by ▴ 80
0
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0
replies
1.6k
views
New Alzheimer's disease microarray data set available
Microarray BRAIN Microarray BRAIN
20.5 years ago Eric Blalock ▴ 250
0
votes
0
replies
851
views
Overriding maPrintTip method
BRAIN BRAIN
20.9 years ago Kellie J. Archer, Ph.D. ▴ 120
0
votes
0
replies
958
views
Q-value package now available
BRAIN BRAIN
21.1 years ago Warnes, Gregory R ▴ 460
50 results • Page 1 of 1
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find: ```` # estimate d…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species by Jeremy • 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error? by Urotree • 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Votes
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
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