Showing : microarray • reset
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problem with contrast.matrix and eBayes in limma
Microarray Microarray
12.5 years ago Guest User ★ 13k
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Chip-seq pipeline and cloud ami questions
Sequencing Microarray edgeR Sequencing Microarray edgeR
12.5 years ago Christopher Howerton ▴ 40
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analyze three factors in Limma
Microarray limma Microarray limma
updated 12.5 years ago by 53k • written 12.6 years ago by ▴ 20
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1.6k
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PAM: Applying published classifiers
Microarray Microarray
12.6 years ago Ed Siefker ▴ 230
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17
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3.8k
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[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 12.6 years ago by ★ 13k • written 12.6 years ago by ▴ 330
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Add new affy organism platform
Microarray Annotation Organism cdf db0 probe annotate affy Microarray Annotation cdf
updated 12.6 years ago by ★ 7.2k • written 12.6 years ago by ▴ 50
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ABarray error
Microarray Annotation GO limma beadarray Microarray Annotation GO limma beadarray
12.6 years ago Mani, Jay ▴ 20
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Agilent 8x60K Gene Expression Package
Microarray Normalization limma Microarray Normalization limma
12.6 years ago Gordon Smyth 53k
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1.8k
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Agilent 8x60K Gene Expression Package
Microarray Normalization Microarray Normalization
12.6 years ago Vandana Sandhu ▴ 10
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1
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1.5k
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Unexpected output from Limma background subtraction & Normalization
Microarray Normalization limma marray puma Microarray Normalization limma marray puma
updated 4.8 years ago by 53k • written 12.6 years ago by ▴ 20
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Lumi problem - 'Annotation columns not available'
Microarray GO illuminaMousev1 Microarray GO illuminaMousev1
updated 12.6 years ago by ▴ 440 • written 12.6 years ago by ▴ 310
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ComBat - question about normalization method
Microarray Normalization probe Microarray Normalization probe
12.6 years ago W. Evan Johnson ▴ 870
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Differentially expressed genes from specific cell types from a single sample
Microarray GO Microarray GO
12.6 years ago Guest User ★ 13k
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Quantiles from virtualArray example without batcheffect removal are all the same
Microarray BatchEffect hgu133plus2 hgug4112a virtualArray Microarray BatchEffect hgug4112a
12.6 years ago Daniel Emden ▴ 10
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1
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1.4k
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Unexpected Results from Limma background subtraction & marray normalizatoin
Microarray Normalization limma marray Microarray Normalization limma marray
updated 4.8 years ago by 53k • written 12.6 years ago by ▴ 20
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2
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1.5k
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Microarray Analysis of Rat Gene 2.0 ST arrays
Microarray cdf Microarray cdf
updated 12.6 years ago by 68k • written 12.6 years ago by ★ 13k
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Normalizing a dataset from GEO to suit a classifier trained on another dataset
Microarray Normalization Preprocessing probe affy preprocessCore frma Microarray probe
12.6 years ago Matthew McCall ▴ 830
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1.4k
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Normalizing a dataset from GEO to suit a classifier trained on another dataset
Microarray probe Microarray probe
updated 12.6 years ago by ▴ 830 • written 12.6 years ago by ★ 13k
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2.5k
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Question on unbalanced paired design
Microarray Normalization GO limma DOSE Microarray Normalization GO limma DOSE
updated 12.7 years ago by ★ 7.9k • written 12.7 years ago by ▴ 40
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Bioconductor Digest, Vol 122, Issue 5
Microarray convert sva Microarray convert sva
12.7 years ago W. Evan Johnson ▴ 870
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1.1k
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A question about the gage package
Microarray probe gage Microarray probe gage
12.7 years ago Luo Weijun ★ 1.6k
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802
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Homoscedasticity
Microarray Microarray
12.7 years ago Guest User ★ 13k
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1.6k
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Analyzing "differential variability" of methylation (and gene expression)
Microarray Microarray
updated 12.7 years ago by ▴ 190 • written 12.7 years ago by ▴ 190
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0
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sva: No significant surrogate variables
Microarray sva Microarray sva
12.7 years ago Shraddha Pai ▴ 80
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1
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1.4k
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enquiry about the limma script
Microarray limma Microarray limma
updated 12.7 years ago by 53k • written 12.7 years ago by ▴ 10
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Estimate how much a factor contributes to the variation
Microarray Cancer Microarray Cancer
updated 12.7 years ago by ★ 4.1k • written 12.7 years ago by ▴ 10
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A question about the gage package
Microarray probe gage Microarray probe gage
12.7 years ago He, Yiwen NIH/CIT ▴ 360
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1.4k
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CAMDA 2013 Challenge: Big Data in Life Sciences
Sequencing Microarray Genetics Classification Clustering Regression Sequencing Microarray
12.7 years ago CAMDA 2013 ▴ 30
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2
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1.6k
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ChIPpeakAnno query
Microarray Annotation Cancer Prostate annotate affy convert biomaRt ChIPpeakAnno Cancer
updated 12.7 years ago by ▴ 10 • written 12.7 years ago by ★ 4.3k
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assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
12.7 years ago Julie Zhu ★ 4.3k
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892
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Why Gene Set Enrichment results of two data set of the same disease are very different?
Microarray Microarray
updated 12.7 years ago by 21k • written 12.7 years ago by ▴ 110
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Bioconductor Digest, Vol 121, Issue 13
RNASeq Microarray Normalization GO Classification Clustering Cancer Mus musculus probe GO
12.7 years ago Matthew Thornton ▴ 390
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2
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1.2k
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time course analyses Illumina RNA-seq data
Microarray Microarray
updated 12.7 years ago by ★ 13k • written 12.7 years ago by ▴ 10
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3.1k
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ComBat: How to choose multiple covariates in ComBat analysis- Need advice
Microarray Microarray
12.8 years ago W. Evan Johnson ▴ 870
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2
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1.5k
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ComBat: How to choose multiple covariates in ComBat analysis- Need advice
Microarray Microarray
12.8 years ago hu duan ▴ 30
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0
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919
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Reminder - VIB Nucleomics Core - User Meeting 2013
Sequencing Microarray Sequencing Microarray
12.8 years ago Rudy van Eijsden ▴ 40
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1.8k
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GSVA
Microarray Pathways GSVA Microarray Pathways GSVA
12.8 years ago Robert Castelo ★ 3.4k
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AgiMicroRna for new Agilent Chip format
Microarray GO limma PROcess microRNA AgiMicroRna Microarray GO limma PROcess microRNA
12.8 years ago Gordon Smyth 53k
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1.5k
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miRNA analysis advice
miRNA Microarray microRNA miRNA Microarray microRNA
updated 12.8 years ago by 68k • written 12.8 years ago by ▴ 70
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1.1k
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Design question: How to account for dependent samples?
Microarray Microarray
updated 12.8 years ago by 53k • written 12.8 years ago by ▴ 100
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1.6k
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Detecting significant trends in variability
Microarray Preprocessing probe minfi Microarray Preprocessing probe minfi
12.8 years ago Gustavo Fernández Bayón ▴ 440
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2
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1.5k
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Fwd: Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray Preprocessing BSgenome BSgenome MEDIPS Microarray Preprocessing BSgenome MEDIPS
updated 12.8 years ago by ▴ 290 • written 12.8 years ago by ▴ 570
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953
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Error in sqliteExecStatement(con, statement, bind.data)
Microarray ChipName oligo Microarray ChipName oligo
12.8 years ago Guest User ★ 13k
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1
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2.5k
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Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
12.8 years ago Matthew Thornton ▴ 390
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3
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1.5k
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How to make a db package for Agilent-015354 Bovine Oligo Microarray (4x44K)?
Microarray Annotation oligo Microarray Annotation oligo
updated 12.8 years ago by ▴ 140 • written 12.8 years ago by ★ 13k
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6
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1.5k
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Extract microarray data for genes identified by GO analysis
Microarray GO Category Microarray GO Category
updated 12.8 years ago by 68k • written 12.8 years ago by ★ 13k
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12
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8.2k
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Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray GO oligo AnnotationForge Microarray GO oligo AnnotationForge
12.8 years ago James W. MacDonald 68k
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0
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966
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Segfault in MEDIPS MEDIPS.methylProfiling() with ROI file
Microarray BSgenome BSgenome MEDIPS Microarray BSgenome BSgenome MEDIPS
12.8 years ago Stephen Turner ▴ 290
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1
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1.2k
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Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray oligo Microarray oligo
updated 12.8 years ago by ★ 7.2k • written 12.8 years ago by ★ 13k
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1.6k
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structure of cfx file for HTqPCR
Microarray qPCR cycle HTqPCR Microarray qPCR cycle HTqPCR
12.8 years ago Guest User ★ 13k
2,319 results • Page 17 of 47
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Comment: 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 …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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