Showing : microarray • reset
33
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0
replies
45k
views
limma moderated t-statistics and B-statistics
Microarray limma
21.3 years ago • updated 5.2 years ago Gordon Smyth 53k
2
votes
5
replies
32k
views
Row labels in a heatmap
Microarray Microarray
updated 13.5 years ago by 68k • written 13.5 years ago by ▴ 60
0
votes
2
replies
27k
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Installing EnhancedVolcano package in R
microarray software error
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by • 0
0
votes
0
replies
20k
views
1000 R tutorials/Links
Sequencing Microarray Genetics Visualization Network Bayesian Classification Clustering
15.6 years ago David Lyon ▴ 340
0
votes
10
replies
18k
views
Fine tuning heatmap.2 graphics
Microarray Microarray
updated 19.9 years ago by ▴ 290 • written 19.9 years ago by ▴ 70
7
votes
1
reply
17k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 2.9 years ago by • 0 • written 11.7 years ago by ▴ 40
0
votes
7
replies
17k
views
How to adjust the Heatmap.2 color key
Microarray GeneSpring Microarray GeneSpring
17.5 years ago Martin Bonke ▴ 40
2
votes
5
replies
16k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 12.0 years ago by 68k • written 12.0 years ago by ▴ 390
0
votes
6
replies
14k
views
Package version of Bioconductor cannot be unloaded, Error in unloadNamespace(package),help!!
microarray software error hgu133plus2.db
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
1
vote
12
replies
14k
views
Using limma for quantitative proteomics data
Microarray Proteomics limma Microarray Proteomics limma
13.6 years ago Yong Li ▴ 80
28
votes
8
replies
14k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 8.3 years ago by 53k • written 10.8 years ago by ▴ 160
5
votes
2
replies
13k
views
lowess vs. loess
Microarray Normalization
updated 9.7 years ago by 53k • written 22.4 years ago by ▴ 30
4
votes
8
replies
13k
views
how to use idat file for analyses in bioconductor
microarray illumina idat
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 10
6
votes
1
reply
12k
views
How to combine multiple probes representing a single gene?
microarray affy eset
updated 8.9 years ago by 53k • written 8.9 years ago by ▴ 20
17
votes
8
replies
12k
views
remove microarray batch effects using Limma
Microarray
updated 19 months ago by 53k • written 15.2 years ago by ▴ 120
5
votes
8
replies
11k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 21 months ago by • 0 • written 9.4 years ago by ▴ 30
8
votes
15
replies
11k
views
Design matrix for continuous independent variable in limma
limma microarray
10.0 years ago Linda Chaba ▴ 10
0
votes
2
replies
11k
views
problems with "cannot allocate vector of size.."
Microarray gcrma Microarray gcrma
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 70
1
vote
7
replies
10k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 3.8 years ago by • 0 • written 7.0 years ago by ▴ 10
0
votes
0
replies
9.9k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a
11.6 years ago Guest User ★ 13k
13
votes
9
replies
9.7k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
10.8 years ago svlachavas ▴ 840
0
votes
4
replies
9.5k
views
Agilent 2-color Microarray data analysis tutorial
Microarray Visualization Clustering Microarray Visualization Clustering
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 140
2
votes
2
replies
9.5k
views
Convert Expression Set into a Matrix or Data Frame
microarray biobase affy R
updated 10.0 years ago by ▴ 760 • written 10.0 years ago by • 0
3
votes
2
replies
9.2k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 3.1 years ago by ▴ 200 • written 8.1 years ago by • 0
0
votes
12
replies
8.6k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray GO oligo AnnotationForge Microarray GO oligo AnnotationForge
12.9 years ago James W. MacDonald 68k
0
votes
2
replies
8.6k
views
heatmap.2 function and the scale option
Microarray Clustering Microarray Clustering
updated 14.3 years ago by ▴ 80 • written 14.3 years ago by ▴ 560
0
votes
18
replies
8.0k
views
WGCNA error in network construction ?
microarray rnaseq
8.8 years ago m.azhar ▴ 10
0
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4
replies
8.0k
views
Limma Volcano Plot Highlight Top Genes by Color
limma microarray volcanoplot color
updated 7.3 years ago by 53k • written 7.3 years ago by • 0
4
votes
7
replies
7.9k
views
Annotating HTA 2.0 genes
microarray
11.2 years ago statistuta • 0
0
votes
3
replies
7.6k
views
Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
Microarray Normalization Microarray Normalization
updated 17.8 years ago by ★ 13k • written 17.8 years ago by ▴ 20
2
votes
10
replies
7.6k
views
Probeset ID's to entrez for Clariom D Human Affy Array
microarray affy
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
3
votes
2
replies
7.5k
views
error with accessing GEOquery data
Microarray Microarray
updated 16.4 years ago by 21k • written 16.4 years ago by ▴ 340
9
votes
4
replies
7.5k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
8.8 years ago Anna ▴ 50
5
votes
9
replies
7.4k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray affy
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 40
1
vote
2
replies
7.3k
views
explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 10.5 years ago by ★ 29k • written 10.5 years ago by ▴ 10
0
votes
1
reply
7.3k
views
plotting 3d image of pca analysis
Microarray Microarray
updated 15.6 years ago by ▴ 430 • written 15.6 years ago by ▴ 40
0
votes
2
replies
7.2k
views
gplots Heatmap
SNP Transcription Sequencing RNASeq miRNA Microarray Annotation Normalization GO Cancer
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 10
2
votes
4
replies
6.8k
views
T-test for microarray data
limma microarray t.test
updated 10.9 years ago by 25k • written 10.9 years ago by • 0
4
votes
14
replies
6.5k
views
Including technical and biological replicates in Limma block analysis?
limma microarray block paired linear model
11.1 years ago vas ▴ 40
0
votes
2
replies
6.5k
views
How to read bgx files in R
microarray annotation illumina
10.5 years ago kanacska ▴ 10
5
votes
11
replies
6.4k
views
Duplicate gene ID's returned from limma microarray analysis
limma microarray
updated 3.7 years ago by 53k • written 9.0 years ago by ▴ 80
0
votes
3
replies
6.4k
views
median normalization
Microarray Normalization Microarray Normalization
updated 14.4 years ago by 68k • written 14.4 years ago by ▴ 580
6
votes
6
replies
6.3k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 5.9 years ago by 53k • written 5.9 years ago by ▴ 50
1
vote
4
replies
6.3k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 3.1 years ago by • 0
0
votes
2
replies
6.1k
views
microarray: dealing with multi probes for one gene
Microarray limma Microarray limma
updated 18.7 years ago by ★ 1.3k • written 18.7 years ago by ▴ 10
8
votes
10
replies
6.1k
views
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
limma topTable confidence interval effect size microarray
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 90
0
votes
3
replies
6.1k
views
limma design and contrast matrix for paired experiment
Microarray limma edgeR Microarray limma edgeR
13.0 years ago Gordon Smyth 53k
0
votes
2
replies
6.0k
views
sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 12.4 years ago by 53k • written 12.4 years ago by ▴ 120
1
vote
12
replies
5.9k
views
EdgeR: replicated pools, yes or not?
RNASeq Microarray edgeR RNASeq Microarray edgeR
updated 11.7 years ago by ★ 7.9k • written 11.7 years ago by ★ 13k
9
votes
10
replies
5.9k
views
Simple significance test functions from R packages limma and plsgenomics
limma plsgenomics microarray differential gene expression
updated 11.0 years ago by 53k • written 11.0 years ago by ▴ 10
2,319 results • Page 1 of 47
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Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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