Showing : cancer • reset
0
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4
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1.3k
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limma design question
Microarray Cancer limma Microarray Cancer limma
updated 17.2 years ago by 68k • written 17.2 years ago by ▴ 330
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2
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1.6k
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Processing data from Illumina HumanCNV370-Quad chips
Cancer Breast Cancer Breast
17.2 years ago Steven McKinney ▴ 310
0
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4
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1.6k
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Course material for "Using Bioconductor for ChIP-seq experiments"
Sequencing Cancer BSgenome annotate Biostrings BSgenome Sequencing Cancer BSgenome
updated 17.2 years ago by ▴ 10 • written 17.2 years ago by ★ 1.6k
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1.5k
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Talk & Poster Call - qPCR 2009 Event
SNP qPCR Normalization Visualization Regression Cancer probe PROcess microRNA SNP qPCR
17.2 years ago qPCR Platform - the reference in real-t… ▴ 170
0
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2
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1.5k
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applying coxfilter after LIMMA
Survival Cancer limma Survival Cancer limma
updated 17.2 years ago by 68k • written 17.2 years ago by ▴ 330
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3
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2.6k
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gene expression data followup
Survival Cancer Survival Cancer
updated 17.2 years ago by 68k • written 17.2 years ago by ▴ 330
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0
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1.4k
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Postdoctoral scientist/programmer positions
Sequencing Cancer Sequencing Cancer
17.2 years ago Crispin Miller ★ 1.1k
0
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4
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2.8k
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biomaRt get exon intron structure of a transcrit
Cancer biomaRt Cancer biomaRt
17.2 years ago Shi, Tao ▴ 720
0
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2
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1.1k
views
Colourful way of visualising differential analysis results
Microarray Cancer limma Microarray Cancer limma
updated 17.2 years ago by ▴ 220 • written 17.2 years ago by ★ 1.9k
0
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4
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1.9k
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CDF issue
Annotation Cancer cdf annotate affy Annotation Cancer cdf annotate affy
17.2 years ago Mathe, Ewy NIH/NCI [F] ▴ 40
0
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0
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765
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BMP4 probe '1940386' missing in illuminaHumanv2BeadID.db (as compared to illuminaHumanv2ProbeID.db)
Annotation Cancer probe annotate Annotation Cancer probe annotate
17.2 years ago Julian Lee ▴ 140
0
votes
18
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3.7k
views
LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
Cancer gcrma LPE affylmGUI Cancer gcrma LPE affylmGUI
updated 17.2 years ago by ▴ 70 • written 17.2 years ago by ★ 13k
0
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0
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1.4k
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Beadarray and illumina methylation arrays
Normalization Cancer beadarray Normalization Cancer beadarray
17.2 years ago Julian Lee ▴ 140
0
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5
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1.7k
views
BMP4 probe '1940386' missing in illuminaHumanv2BeadID.db (as compared to illuminaHumanv2ProbeID.db)
Cancer annotate Cancer annotate
updated 17.2 years ago by ★ 7.2k • written 17.2 years ago by ▴ 140
0
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2
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1.4k
views
LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
Cancer gcrma LPE Cancer gcrma LPE
updated 17.2 years ago by ★ 1.6k • written 17.2 years ago by ▴ 70
0
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1
reply
1.3k
views
Reading ArrayExpress data [was Re: questions on the ImaGene data using limma package]
Annotation Normalization GO Cancer limma ArrayExpress Annotation Normalization GO Cancer
updated 17.2 years ago by ▴ 280 • written 17.2 years ago by 53k
0
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1
reply
1.1k
views
questions on the ImaGene data using limma package
Normalization Cancer limma Normalization Cancer limma
17.2 years ago Ming YI [Contr] ▴ 30
0
votes
4
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1.5k
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Reading ArrayExpress data [was Re: questions on the ImaGene data using limma package]
Annotation Normalization Cancer limma ArrayExpress Annotation Normalization Cancer limma
updated 17.2 years ago by ▴ 30 • written 17.2 years ago by 53k
0
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2
replies
1.9k
views
Error when trying to build a package that needs to import GO.db, GOstats, ath1121501.db packages
Annotation GO Cancer ath1121501 AnnotationDbi BHC Annotation GO Cancer ath1121501 BHC
updated 17.2 years ago by ▴ 60 • written 17.2 years ago by 25k
0
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4
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1.3k
views
sequencing workshop
Cancer Cancer
updated 17.2 years ago by ★ 1.6k • written 17.3 years ago by ★ 5.5k
0
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0
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1.5k
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[Fwd: batch info for cellHTS]
GO Cancer cellHTS cellHTS2 GO Cancer cellHTS cellHTS2
17.2 years ago Florian Hahne ▴ 540
0
votes
8
replies
1.5k
views
Limma contrasts question
Cancer Cancer
updated 17.3 years ago by 68k • written 17.3 years ago by ★ 1.9k
0
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0
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1.3k
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The EMMES Corporation-Statistical Analyst position
Microarray Cancer Microarray Cancer
17.3 years ago Marcella Pickard ▴ 10
0
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0
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1.2k
views
The us of bioConductor to analyze raw and segmented data from TCGA (The Cancer Genome Atlas)
SNP Cancer SNP Cancer
17.3 years ago Wang, Frank IM, Americas ▴ 10
0
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0
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2.0k
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Postdoc positions at the Cancer Research UK Cambridge Research Institute
SNP Genetics Pathways Cancer CGH microRNA SNP Genetics Pathways Cancer CGH microRNA
17.3 years ago Florian Markowetz ▴ 20
0
votes
2
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1.6k
views
CGHcall error
aCGH Normalization Cancer aCGH CGHcall copynumber aCGH Normalization Cancer aCGH CGHcall
updated 17.3 years ago by ▴ 110 • written 17.3 years ago by ▴ 40
0
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0
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1.3k
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problem installing affycoretools in R in linux environment
GO Cancer biomaRt affycoretools GO Cancer biomaRt affycoretools
17.3 years ago rgentleman ★ 5.5k
0
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1
reply
1.1k
views
How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
Cancer hgu95av2 affy Cancer hgu95av2 affy
updated 17.3 years ago by ▴ 360 • written 17.3 years ago by 25k
0
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0
replies
1.2k
views
spiked controls wrong order on samples wit 2 rounds of amplification normalize with GCRMA
Microarray Cancer affy gcrma affyPLM Microarray Cancer affy gcrma affyPLM
17.3 years ago Richard Friedman ★ 2.0k
0
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4
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1.7k
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How do you keep track of your analyses
Cancer Cancer
updated 17.3 years ago by ▴ 60 • written 17.3 years ago by ★ 1.9k
0
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1
reply
893
views
Bioconductor and sequencing
Sequencing Cancer Sequencing Cancer
updated 17.3 years ago by ▴ 150 • written 17.3 years ago by ★ 5.5k
0
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0
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1.2k
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Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)
Annotation GO Cancer GOstats biomaRt Annotation GO Cancer GOstats biomaRt
17.3 years ago Emmanuel Levy ▴ 270
0
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2
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1.5k
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biomart doesn't annotate all the genes queried -CEACAM6
Cancer hgu133plus2 annotate affy biomaRt Cancer hgu133plus2 annotate affy biomaRt
17.3 years ago Julian Lee ▴ 140
1
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0
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1.2k
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SIM new package for Statistical Integration of Microarrays
SNP Microarray Visualization Cancer SNP Microarray Visualization Cancer
17.3 years ago Maarten van Iterson ▴ 60
0
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1
reply
1.2k
views
kinexus antibody arrays
Cancer Cancer
17.4 years ago • updated 17.3 years ago Richard Friedman ★ 2.0k
0
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0
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982
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Pd info package affy 10K array
Microarray Annotation Cancer cdf probe affy Microarray Annotation Cancer cdf probe affy
17.3 years ago Henrik Bengtsson ★ 2.4k
0
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1
reply
1.8k
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arrayQualityMetrics - how do I use this with an MAList object???
Cancer convert arrayQualityMetrics Cancer convert arrayQualityMetrics
updated 17.3 years ago by ▴ 680 • written 17.4 years ago by 25k
0
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1
reply
1.4k
views
Agilent Human Genome CGH 44K annotation
Annotation Cancer CGH Annotation Cancer CGH
updated 17.4 years ago by 21k • written 17.4 years ago by ★ 1.9k
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0
replies
1.0k
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Using limma for omnibus F tests
Cancer limma Cancer limma
17.4 years ago Gordon Smyth 53k
0
votes
2
replies
1.7k
views
LOH analysis for illumina data
SNP Cancer Prostate SNP Cancer Prostate
17.4 years ago Yu Chuan Tai ▴ 440
0
votes
1
reply
963
views
RMAGEML installation and ArrayExpress database
Cancer RMAGEML ArrayExpress Cancer RMAGEML ArrayExpress
17.4 years ago Martin Morgan 25k
0
votes
1
reply
1.2k
views
ANNOUNCEMENT: 20% Discount on Books from Chapman & Hall/CRC!
Proteomics Cancer Proteomics Cancer
17.5 years ago • updated 17.4 years ago Thomas, Judy ▴ 40
0
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1
reply
1.5k
views
library(affyQCReport)-NA(arg1); arrayQualityMetrics-no end
Cancer cdf affy simpleaffy affyQCReport affyio arrayQualityMetrics Cancer cdf affy
updated 17.4 years ago by ★ 5.5k • written 17.4 years ago by ▴ 200
0
votes
4
replies
1.8k
views
Quality control;Missing value;installation
Cancer cdf affy affyQCReport affyio arrayQualityMetrics Cancer cdf affy affyQCReport
updated 17.4 years ago by ★ 5.5k • written 17.4 years ago by ▴ 200
0
votes
2
replies
1.7k
views
Adding a text label to the classvec colour bar in heatplot
Clustering Cancer graph GLAD Clustering Cancer graph GLAD
updated 17.5 years ago by ▴ 460 • written 17.5 years ago by ★ 6.5k
0
votes
0
replies
1.3k
views
Is anyone developing an extensible Galaxy-like interface for Bioconductor?
Cancer affylmGUI limmaGUI Cancer affylmGUI limmaGUI
17.5 years ago Martin Morgan 25k
0
votes
4
replies
2.1k
views
Adding a text label to the classvec colour bar in heatplot
Clustering Cancer graph Clustering Cancer graph
updated 17.5 years ago by ▴ 460 • written 17.5 years ago by ▴ 510
0
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0
replies
1.5k
views
confusion about nomenclature of illumina annotationpackages
BiocViews Annotation Cancer Mus musculus illuminaHumanv1 illuminaHumanv2 probe annotate
17.5 years ago Lynn Amon ▴ 280
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0
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1.6k
views
Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix
Epigenetics Cancer probe affy xps Epigenetics Cancer probe affy xps
17.5 years ago Martin Morgan 25k
0
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3
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1.3k
views
Small RNAs database
Cancer Cancer
updated 17.5 years ago by ★ 13k • written 17.5 years ago by ★ 1.9k
1,555 results • Page 19 of 32
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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