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Showing :
microarray
•
reset
32
votes
0
replies
38k
views
limma moderated t-statistics and B-statistics
Microarray
limma
19.6 years ago • updated 3.5 years ago
Gordon Smyth
50k
28
votes
8
replies
12k
views
Removing continuous covariate effects in limma analysis
limma
microarray
updated 6.6 years ago by
Gordon Smyth
50k • written 9.1 years ago by
Pauly Lin
▴ 150
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 2.7 years ago by
Leanne
• 0 • written 13.5 years ago by
Xie, Zhi NIH/NHLBI [E]
▴ 120
15
votes
14
replies
3.6k
views
extract similar expressed genes (SEGs) rather than DEGs
limma
microarray
updated 9.2 years ago by
Sean Davis
21k • written 9.3 years ago by
Andreas Heider
▴ 340
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma
differential gene expression
microarray
linear model
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
bcbio_uk
▴ 10
12
votes
9
replies
7.9k
views
Appropriate use of the function treat of the limma package
limma
treat
microarray
bioconductor
9.1 years ago
svlachavas
▴ 830
12
votes
7
replies
4.1k
views
illumina ht-12 v4 expression beadchip
microarray
illumina human ht-12 v4
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
arisarkar88
▴ 40
11
votes
5
replies
2.3k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat
idat
microarray
illumina
updated 8.6 years ago by
Mark Cowley
▴ 400 • written 8.6 years ago by
willj
▴ 30
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 7 months ago by
Gordon Smyth
50k • written 5.2 years ago by
tleona3
• 0
10
votes
5
replies
2.3k
views
One replicate (one-color OR two-color) is enough to use Limma?
limma
microarray
7.3 years ago
kevin.m.hao
▴ 10
9
votes
10
replies
4.9k
views
Simple significance test functions from R packages limma and plsgenomics
limma
plsgenomics
microarray
differential gene expression
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
chandlerjd58
▴ 10
9
votes
4
replies
6.3k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray
limma
design and contrast matrix
7.1 years ago
Anna
▴ 50
9
votes
10
replies
2.1k
views
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
limma
microarray
genefilter
deseq2
4.9 years ago
Jurat Shahidin
▴ 80
9
votes
6
replies
3.9k
views
Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options
microarray
oligo
affycoretools
pd.hugene.2.0.st
hugene20sttranscriptcluster.db
updated 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
svlachavas
▴ 830
8
votes
3
replies
3.2k
views
Differing topTable() results with Limma with and without specifying coefficient
limma
microarray
statistics
updated 8.0 years ago by
Gordon Smyth
50k • written 8.0 years ago by
krr
• 0
8
votes
12
replies
4.2k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma
microarray
interaction model
multiple factor design
makeContrasts
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
svlachavas
▴ 830
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
8
votes
11
replies
1.9k
views
Creating design matrix in LIMMA
limma
microarray
R
7.3 years ago
sgblackpearl
• 0
8
votes
5
replies
2.8k
views
Limma un moderated t-test
limma
microarray
updated 8.1 years ago by
Axel Klenk
★ 1.0k • written 8.1 years ago by
chris86
▴ 420
8
votes
8
replies
4.4k
views
Limma: fit a model with duplicateCorrelation()
limma
microarray
duplicatecorrelation
technical replicates
linear model
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
Eleni Christodoulou
▴ 150
8
votes
15
replies
8.7k
views
Design matrix for continuous independent variable in limma
limma
microarray
8.3 years ago
Linda Chaba
▴ 10
7
votes
1
reply
15k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 14 months ago by
yr542
• 0 • written 10.0 years ago by
jesus urbano
▴ 40
7
votes
7
replies
2.0k
views
Identify up and down regulated genes in affymetrix data
limma
microarray
affy
updated 6.8 years ago by
tg369
▴ 40 • written 6.8 years ago by
Jamal
• 0
7
votes
2
replies
1.6k
views
limma experimental design
limma
microarray
updated 8.1 years ago by
Gordon Smyth
50k • written 8.1 years ago by
christopher.clarskon15
▴ 20
7
votes
2
replies
2.2k
views
Appropriate explanation of the methodology behind arrayWeights function from limma R package
limma
arrayWeights
variance
sampleQuality
microarray
updated 8.5 years ago by
Ryan C. Thompson
★ 7.9k • written 8.6 years ago by
svlachavas
▴ 830
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
7
votes
13
replies
1.9k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma
microarray
hugeneST
batch effect
DE
updated 5.3 years ago by
Ryan C. Thompson
★ 7.9k • written 5.3 years ago by
svlachavas
▴ 830
7
votes
8
replies
2.1k
views
Microarray analysis using RMA method using affy, limma
microarray
annotation
aureus
affy
6.3 years ago • updated 6.2 years ago
neranjan007
• 0
7
votes
4
replies
1.6k
views
very high adjusted P-vals using Illumina data from GEO
limma
p values
microarray
illumina
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
Jason
▴ 20
7
votes
6
replies
1.8k
views
Limma import .gpr file error
limma
gpr
microarray
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
Guillaume Robert
• 0
6
votes
6
replies
1.4k
views
Too many differentially expressed miRNA with limma
limma
miRNA
Microarray
17 months ago
Sara
▴ 10
6
votes
4
replies
2.6k
views
Affymetrix miRNA4.1 / oligo package / pd.mirna.4.1
microarray
mirna
oligo package
pdinfobuilder
pd.mirna
updated 4.5 years ago by
soumyab.g
▴ 10 • written 6.9 years ago by
rolan.zauner
▴ 20
6
votes
3
replies
1.4k
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 3.9 years ago by
Sean Davis
21k • written 3.9 years ago by
fabian
▴ 40
6
votes
9
replies
2.3k
views
LIMMA paired analysis adjusting for two continuous variables - microarray data
limma
limma design matrix
limma paired analysis
microarray
7.2 years ago
danielle.newby
• 0
6
votes
2
replies
3.5k
views
Is ComBat introducing a signal where there is none?
Microarray
Clustering
Cancer
limma
Microarray
Clustering
Cancer
limma
10.4 years ago • updated 8.7 years ago
Vegard Nygaard
▴ 110
6
votes
4
replies
2.7k
views
Identification of DEGs through limma analysis
limma
microarray
DEGs
p values
lfc
6.9 years ago
rkp
• 0
6
votes
4
replies
1.2k
views
Limma outputs different results for same sample?
topTable
MicroarrayData
ebayes
limma
Microarray
3.2 years ago
snijesh
▴ 20
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
6
votes
8
replies
1.8k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma
microarray
affy
edger
4.9 years ago
Jurat Shahidin
▴ 80
6
votes
1
reply
11k
views
How to combine multiple probes representing a single gene?
microarray
affy
eset
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
mathavanbioinfo
▴ 20
6
votes
4
replies
3.1k
views
AnnotationData Packages for Agilent microarrays
microarray
annotation
limma
.db
Agilent
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
Alexander Azarian
▴ 30
6
votes
22
replies
3.9k
views
Oligo package: paCalls questions
microarray
oligo
updated 8.9 years ago by
cstrato
★ 3.9k • written 8.9 years ago by
whyuen
▴ 20
6
votes
9
replies
1.6k
views
Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma
illumina
microarray
multifactorial design
batch effect
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Konstantinos Yeles
▴ 80
6
votes
5
replies
1.3k
views
limma & design matrix: for 2-color dyes and 4-comparisons?
limma
microarray
limma design matrix
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Mehmet Ilyas Cosacak
• 0
6
votes
11
replies
2.2k
views
microarray data analsis with limma?
limma
genepix
microarray
agilent microarrays
8.0 years ago
Mehmet Ilyas Cosacak
• 0
6
votes
4
replies
1.7k
views
Weird error with raw data using function boxplot after importing Affymetrix Human ST 2.0 CEL files with oligo
microarray
affymetrix Human ST arrays
oligo
hugene20sttranscriptcluster.db
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
svlachavas
▴ 830
6
votes
6
replies
5.1k
views
Finding enriched pathways from a gene list.
microarray
limma
kegg
ENTREZ
enrichment analysis
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
omarrafiqued
▴ 50
5
votes
10
replies
4.3k
views
Interpretation of results for treat & topTreat functions from limma regarding microarray abalysis
limma
treat
topTreat
microarray
updated 8.0 years ago by
Gordon Smyth
50k • written 8.0 years ago by
svlachavas
▴ 830
5
votes
5
replies
2.7k
views
Joint Preprocessing of RNA-Seq and Microarray datasets
preprocessing
rnaseq
microarray
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
Jo
▴ 30
5
votes
8
replies
1.3k
views
designing matrices practice
limma
microarray
8.1 years ago
christopher.clarskon15
▴ 20
50 results • Page
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Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Votes
package goseq seems to be not available on the latest version of R
package goseq seems to be not available on the latest version of R
Print Differentially Expressed Exons From Dexseq Results
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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