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Showing :
microarray
•
reset
32
votes
0
replies
39k
views
limma moderated t-statistics and B-statistics
Microarray
limma
19.7 years ago • updated 3.6 years ago
Gordon Smyth
50k
2
votes
5
replies
30k
views
Row labels in a heatmap
Microarray
Microarray
updated 11.9 years ago by
James W. MacDonald
66k • written 11.9 years ago by
Liat Shavit Grievink
▴ 60
0
votes
2
replies
22k
views
Installing EnhancedVolcano package in R
microarray
software error
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
kanwal.zahid.siddiqi
• 0
0
votes
0
replies
18k
views
1000 R tutorials/Links
Sequencing
Microarray
Genetics
Visualization
Network
Bayesian
Classification
Clustering
14.0 years ago
David Lyon
▴ 340
0
votes
10
replies
17k
views
Fine tuning heatmap.2 graphics
Microarray
Microarray
updated 18.2 years ago by
Wittner, Ben
▴ 290 • written 18.2 years ago by
Marc Saric
▴ 70
0
votes
7
replies
16k
views
How to adjust the Heatmap.2 color key
Microarray
GeneSpring
Microarray
GeneSpring
15.9 years ago
Martin Bonke
▴ 40
2
votes
5
replies
15k
views
Limma design and contrast matrix question.
Microarray
Regression
limma
Microarray
Regression
limma
updated 10.3 years ago by
James W. MacDonald
66k • written 10.3 years ago by
Matthew Thornton
▴ 360
7
votes
1
reply
15k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 15 months ago by
yr542
• 0 • written 10.1 years ago by
jesus urbano
▴ 40
1
vote
12
replies
13k
views
Using limma for quantitative proteomics data
Microarray
Proteomics
limma
Microarray
Proteomics
limma
11.9 years ago
Yong Li
▴ 80
28
votes
8
replies
12k
views
Removing continuous covariate effects in limma analysis
limma
microarray
updated 6.7 years ago by
Gordon Smyth
50k • written 9.2 years ago by
Pauly Lin
▴ 150
0
votes
6
replies
11k
views
Package version of Bioconductor cannot be unloaded, Error in unloadNamespace(package),help!!
microarray
software error
hgu133plus2.db
updated 5.1 years ago by
Martin Morgan
25k • written 5.1 years ago by
naf
• 0
5
votes
2
replies
11k
views
lowess vs. loess
Microarray
Normalization
updated 8.0 years ago by
Gordon Smyth
50k • written 20.7 years ago by
nataraja@mit.edu
▴ 30
6
votes
1
reply
11k
views
How to combine multiple probes representing a single gene?
microarray
affy
eset
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
mathavanbioinfo
▴ 20
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 2.8 years ago by
Leanne
• 0 • written 13.6 years ago by
Xie, Zhi NIH/NHLBI [E]
▴ 120
4
votes
8
replies
10k
views
how to use idat file for analyses in bioconductor
microarray
illumina
idat
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
kritikamish99
▴ 10
0
votes
2
replies
10k
views
problems with "cannot allocate vector of size.."
Microarray
gcrma
Microarray
gcrma
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
Manuela Di Russo
▴ 70
0
votes
4
replies
8.9k
views
Agilent 2-color Microarray data analysis tutorial
Microarray
Visualization
Clustering
Microarray
Visualization
Clustering
updated 14.4 years ago by
Martin Morgan
25k • written 14.4 years ago by
Chuming Chen
▴ 140
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 4 weeks ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
0
votes
0
replies
8.9k
views
virtualArray vignette does not work: 'data' must be of a vector type, was 'NULL'
Microarray
Annotation
Preprocessing
hgu133plus2
hgug4112a
virtualArray
Microarray
hgug4112a
10.0 years ago
Guest User
★ 13k
8
votes
15
replies
8.8k
views
Design matrix for continuous independent variable in limma
limma
microarray
8.4 years ago
Linda Chaba
▴ 10
0
votes
2
replies
8.0k
views
heatmap.2 function and the scale option
Microarray
Clustering
Microarray
Clustering
updated 12.6 years ago by
Aleš Maver
▴ 80 • written 12.7 years ago by
john herbert
▴ 560
12
votes
9
replies
8.0k
views
Appropriate use of the function treat of the limma package
limma
treat
microarray
bioconductor
9.2 years ago
svlachavas
▴ 830
2
votes
2
replies
8.0k
views
Convert Expression Set into a Matrix or Data Frame
microarray
biobase
affy
R
updated 8.3 years ago by
Diego Diez
▴ 760 • written 8.3 years ago by
hshabbeer.09
• 0
1
vote
7
replies
7.8k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray
normalization
oligo HTA
updated 2.2 years ago by
Harald
• 0 • written 5.3 years ago by
RV
▴ 10
0
votes
4
replies
6.9k
views
Limma Volcano Plot Highlight Top Genes by Color
limma
microarray
volcanoplot
color
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
dmm204
• 0
0
votes
3
replies
6.9k
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 16.2 years ago by
Wolfgang Huber
★ 13k • written 16.2 years ago by
Suprabhath Reddy Gajjala
▴ 20
3
votes
2
replies
6.7k
views
error with accessing GEOquery data
Microarray
Microarray
updated 14.7 years ago by
Sean Davis
21k • written 14.7 years ago by
Kishor Tappita
▴ 340
0
votes
7
replies
6.7k
views
Annotating HTA 2.0 genes
microarray
9.5 years ago
statistuta
• 0
0
votes
1
reply
6.5k
views
plotting 3d image of pca analysis
Microarray
Microarray
updated 14.0 years ago by
Kevin Coombes
▴ 430 • written 14.0 years ago by
Frederico Arnoldi
▴ 40
1
vote
2
replies
6.3k
views
How to convert Illumina HT_12_v4 annotation
convert
R
annotation
microarray
illumina human ht-12 v4
updated 17 months ago by
snijesh
▴ 20 • written 6.5 years ago by
p_donchev84
• 0
9
votes
4
replies
6.3k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray
limma
design and contrast matrix
7.2 years ago • updated 7.1 years ago
Anna
▴ 50
2
votes
4
replies
6.2k
views
T-test for microarray data
limma
microarray
t.test
updated 9.2 years ago by
Martin Morgan
25k • written 9.2 years ago by
eslamias
• 0
2
votes
10
replies
6.2k
views
Probeset ID's to entrez for Clariom D Human Affy Array
microarray
affy
updated 7.7 years ago by
James W. MacDonald
66k • written 7.7 years ago by
jayme.rickman
• 0
0
votes
18
replies
5.9k
views
WGCNA error in network construction ?
microarray
rnaseq
7.2 years ago
m.azhar
▴ 10
0
votes
3
replies
5.8k
views
median normalization
Microarray
Normalization
Microarray
Normalization
updated 12.8 years ago by
James W. MacDonald
66k • written 12.8 years ago by
viritha kaza
▴ 580
1
vote
2
replies
5.8k
views
explanation of makeContrasts function of limma package
limma
microarray
R
geneexpression
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
elisa.micarelli
▴ 10
0
votes
3
replies
5.6k
views
limma design and contrast matrix for paired experiment
Microarray
limma
edgeR
Microarray
limma
edgeR
11.4 years ago
Gordon Smyth
50k
4
votes
14
replies
5.5k
views
Including technical and biological replicates in Limma block analysis?
limma
microarray
block
paired
linear model
9.5 years ago • updated 9.4 years ago
vas
▴ 40
0
votes
12
replies
5.4k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray
GO
oligo
AnnotationForge
Microarray
GO
oligo
AnnotationForge
11.3 years ago
James W. MacDonald
66k
0
votes
2
replies
5.4k
views
How to read bgx files in R
microarray
annotation
illumina
8.9 years ago
kanacska
▴ 10
0
votes
2
replies
5.4k
views
microarray: dealing with multi probes for one gene
Microarray
limma
Microarray
limma
updated 17.0 years ago by
Francois Pepin
★ 1.3k • written 17.0 years ago by
Christophe Boutte
▴ 10
0
votes
2
replies
5.3k
views
sva + voom + limma
RNASeq
Microarray
sva
RNASeq
Microarray
sva
updated 10.7 years ago by
Gordon Smyth
50k • written 10.7 years ago by
Meritxell Oliva
▴ 120
6
votes
6
replies
5.1k
views
Finding enriched pathways from a gene list.
microarray
limma
kegg
ENTREZ
enrichment analysis
updated 4.3 years ago by
Gordon Smyth
50k • written 4.3 years ago by
omarrafiqued
▴ 50
7
votes
8
replies
5.1k
views
Model matrix for anova in limma
limma design matrix
microarray
limma
updated 8.3 years ago by
Steve Lianoglou
★ 13k • written 8.4 years ago by
serpalma.v
▴ 60
0
votes
2
replies
5.1k
views
Packages not getting installed
Microarray
GO
annotate
Microarray
GO
annotate
updated 15.0 years ago by
James W. MacDonald
66k • written 15.0 years ago by
Ashwin Kumar
▴ 90
9
votes
10
replies
5.0k
views
Simple significance test functions from R packages limma and plsgenomics
limma
plsgenomics
microarray
differential gene expression
updated 9.4 years ago by
Gordon Smyth
50k • written 9.4 years ago by
chandlerjd58
▴ 10
5
votes
11
replies
4.9k
views
Duplicate gene ID's returned from limma microarray analysis
limma
microarray
updated 2.1 years ago by
Gordon Smyth
50k • written 7.4 years ago by
mat149
▴ 70
8
votes
10
replies
4.9k
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 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
Konstantinos Yeles
▴ 80
0
votes
2
replies
4.8k
views
gplots Heatmap
SNP
Transcription
Sequencing
RNASeq
miRNA
Microarray
Annotation
Normalization
GO
Cancer
updated 12.3 years ago by
Wolfgang Huber
★ 13k • written 12.3 years ago by
Polikepahad, Sumanth
▴ 10
6
votes
10
replies
4.8k
views
defining a function for multiple paired t.test in many rows of a microarray dataset
microarray
r
t.test
bioconductor
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
svlachavas
▴ 830
50 results • Page
1 of 1
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Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
BioinfGuru
▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0
by
Maximus
• 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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