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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
updated 7 weeks ago by 52k • written 16.6 years ago by ▴ 10
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1.6k
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Creating a model matrix for three age groups using two-colour arrays
Microarray BRAIN Microarray BRAIN
updated 4.6 years ago by 52k • written 16.8 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
6.4 years ago hjaarop1 • 0
0
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1
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1.4k
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CAGEr - How to change plot axis range in CAGEr
BRAIN CAGEr BRAIN CAGEr
updated 7.3 years ago by ▴ 180 • written 11.1 years ago by ▴ 10
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How to proceed with different degradation levels of RNA-seq samples?
degradation RNA-seq variability differential expression brain
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 90
0
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9
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3.4k
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frma and alternative CDFs
GO cdf frma BRAIN GO cdf frma BRAIN
updated 11.1 years ago by ▴ 830 • written 11.1 years ago by ★ 13k
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Job reminder: Open position for a Core Bioinformatician in Lund, Sweden
Microarray BRAIN Microarray BRAIN
12.1 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
12.2 years ago _Bio - Informatics ▴ 20
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Error in example from biomaRt vignette
biomaRt BRAIN biomaRt BRAIN
12.3 years ago Steffen Durinck ▴ 90
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Tukey\'s HSD after ANOVA
GO BRAIN GO BRAIN
12.3 years ago Guest User ★ 13k
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925
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Differentially regulated genes
BRAIN BRAIN
12.5 years ago Ali Mohammadian ▴ 290
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1.5k
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log2 and rowMeans a problem?
BRAIN BRAIN
updated 12.8 years ago by ★ 4.3k • written 12.8 years ago by ▴ 20
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3
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1.5k
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edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
updated 13.2 years ago by 25k • written 13.2 years ago by 52k
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edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
13.2 years ago alessandro.guffanti@genomnia.com ▴ 330
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1.5k
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Three tenure track assistant professorship openings at Inst. Behavioral Genetics, University of Colorado Boulder
Genetics BRAIN Genetics BRAIN
13.4 years ago Matthew Keller ▴ 100
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0
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1.1k
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What is the difference of layout between genepix scanner & agilent scanner
limma BRAIN limma BRAIN
13.9 years ago 이선재 ▴ 30
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1.5k
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[question] integration of microarray data from different sources in limma package
Microarray limma BRAIN Microarray limma BRAIN
updated 13.9 years ago by ▴ 340 • written 13.9 years ago by ▴ 30
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1.2k
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[question] integration of microarray data from different sources in limma package
Microarray limma BRAIN Microarray limma BRAIN
updated 13.9 years ago by ▴ 150 • written 13.9 years ago by ▴ 30
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7
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EBS volumes with the Bioconductor AMI: how to change default behaviour
PROcess BRAIN PROcess BRAIN
14.1 years ago Dan Tenenbaum ★ 8.2k
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EBS volumes with the Bioconductor AMI: how to change default behaviour
BRAIN BRAIN
14.1 years ago Quin Wills ▴ 80
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3.3k
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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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1000
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How to: design matrices for multi organism parts experiment
Organism BRAIN Organism BRAIN
14.3 years ago Hans ▴ 10
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3
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1.7k
views
How to filter a list of SNPs?
BRAIN BRAIN
updated 14.3 years ago by ★ 13k • written 14.3 years ago by ▴ 450
0
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1
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2.0k
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Modeling of methylation status using lumi
Microarray lumi BRAIN Microarray lumi BRAIN
updated 14.5 years ago by ▴ 80 • written 14.5 years ago by ▴ 620
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1.2k
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Modeling of methylation status using lumi
Microarray lumi BRAIN Microarray lumi BRAIN
14.7 years ago Pan Du ★ 1.2k
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1.5k
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Microarray experiments with Drosophilas (miniscule amounts of RNA, cheap organisms)
Microarray BRAIN Microarray BRAIN
updated 14.9 years ago by ▴ 10 • written 14.9 years ago by ▴ 40
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1.0k
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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
16.6 years ago Gordon Smyth 52k
0
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3
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1.5k
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problems with paired design in limma
Microarray BRAIN Microarray BRAIN
16.8 years ago Michael Walter ▴ 160
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Creating a model matrix for three age groups using two-colour arrays
Microarray limma BRAIN Microarray limma BRAIN
16.8 years ago Gordon Smyth 52k
0
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4
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2.2k
views
allen brain atlas
Genetics Annotation BRAIN Genetics Annotation BRAIN
updated 17.0 years ago by 25k • written 17.0 years ago by ▴ 60
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959
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MAQC samples on Affymarix Exon array
BRAIN BRAIN
17.1 years ago Weiyin Zhou ▴ 20
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5
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1.7k
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P-values for tissue specific genes
BRAIN BRAIN
17.1 years ago Pascal Gellert ▴ 30
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1
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1.3k
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new lumi and miRNA array data
Microarray Normalization lumi BRAIN Microarray Normalization lumi BRAIN
updated 17.3 years ago by ★ 13k • written 17.3 years ago by ▴ 830
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2
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1.9k
views
new topGO results using GO.db very different from old ones using GO
GO annotate topGO BRAIN GO annotate topGO BRAIN
updated 17.4 years ago by ▴ 400 • written 17.4 years ago by ▴ 730
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1.0k
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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
18.2 years ago Neddy ▴ 10
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Undergraduate Student Project Summer 2007, at EBI: the synapse and the brain
Pathways BRAIN Pathways BRAIN
18.5 years ago Wolfgang Huber ★ 13k
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read.maimages broken (limma 2.9.10)?
limma BRAIN limma BRAIN
18.6 years ago Gordon Smyth 52k
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0
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961
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read.maimages broken (limma 2.9.10)?
BRAIN BRAIN
18.6 years ago Koen Bossers ▴ 10
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1.4k
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microarray analysis of a dose response * strain experiment
Microarray affy limma maSigPro DOSE BRAIN Microarray affy limma maSigPro DOSE BRAIN
18.8 years ago Naomi Altman ★ 6.0k
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4
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1.9k
views
microarray analysis of a dose response * strain experiment
affy DOSE BRAIN affy DOSE BRAIN
updated 18.8 years ago by 21k • written 18.8 years ago by ▴ 890
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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
19.0 years ago k. brand ▴ 420
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1
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1.3k
views
GCRMA
Microarray Preprocessing gcrma BRAIN Microarray Preprocessing gcrma BRAIN
updated 19.6 years ago by ★ 2.0k • written 19.6 years ago by ▴ 20
0
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3
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1.8k
views
LIMMA lmscFit: difference between linear models
BRAIN BRAIN
20.0 years ago • updated 19.9 years ago Koen Bossers ▴ 20
0
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3
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1.4k
views
limma design matrix
affy BRAIN affy BRAIN
updated 20.7 years ago by ▴ 720 • written 20.7 years ago by ▴ 250
0
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1
reply
1.6k
views
Cluster analysis distance measuer
Microarray Annotation Normalization Clustering Cancer affy limma AnnBuilder BRAIN Cancer
updated 20.8 years ago by ▴ 110 • written 20.8 years ago by ▴ 250
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0
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1.1k
views
help with limma contrast matrix
BRAIN BRAIN
20.8 years ago Kimpel, Mark W ▴ 890
0
votes
3
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1.8k
views
human tissue specific genes
BRAIN BRAIN
updated 21.1 years ago by 21k • written 21.1 years ago by ▴ 80
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0
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1.7k
views
New Alzheimer's disease microarray data set available
Microarray BRAIN Microarray BRAIN
21.1 years ago Eric Blalock ▴ 250
0
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0
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925
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Overriding maPrintTip method
BRAIN BRAIN
21.5 years ago Kellie J. Archer, Ph.D. ▴ 120
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1.1k
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Q-value package now available
BRAIN BRAIN
21.7 years ago Warnes, Gregory R ▴ 460
53 results • Page 1 of 2
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Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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