Showing : Limma • reset
18
votes
37
replies
18k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
9.8 years ago • updated 9.7 years ago svlachavas ▴ 840
2
votes
30
replies
4.9k
views
create design matrix when 2 groups of gene-expression data
limma
9.2 years ago • updated 8.9 years ago mheydarpour ▴ 10
6
votes
25
replies
4.2k
views
How to import normalized file (using xps) to limma for differential expressed genes?
xps heatmap limma
updated 9.0 years ago by ★ 3.9k • written 9.0 years ago by ▴ 120
2
votes
25
replies
7.4k
views
How to use Limma to analyze differences among group items without doing pairwise comparisons
limma
8.9 years ago • updated 8.8 years ago sami.pietila • 0
5
votes
25
replies
2.1k
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 11 months ago by 52k • written 12 months ago by ▴ 10
15
votes
23
replies
3.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
12 months ago • updated 11 months ago Chris ▴ 20
13
votes
21
replies
7.1k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
9.5 years ago osa.zuta ▴ 40
9
votes
21
replies
4.2k
views
Error when fitting linear model with technical replicates and blocking variable
limma technical replicates
9.3 years ago Eleni Christodoulou ▴ 150
9
votes
21
replies
6.3k
views
limma - complex design with paired samples, sex and batch effect
limma paired samples complex-design
9.3 years ago • updated 9.2 years ago aec ▴ 90
12
votes
20
replies
2.6k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 9.6 years ago by ★ 28k • written 9.6 years ago by ▴ 840
3
votes
19
replies
4.4k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
8.0 years ago mheydarpour ▴ 10
7
votes
18
replies
9.5k
views
Differential expression analysis: Continuous variables
DESeq EdgeR limma
9.5 years ago Radek ▴ 90
20
votes
18
replies
5.6k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 9.5 years ago by ▴ 870 • written 9.5 years ago by ▴ 840
5
votes
18
replies
2.3k
views
Difference of difference, paired design
edger deseq2 limma
updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by • 0
12
votes
18
replies
6.6k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 4.0 years ago by 52k • written 4.5 years ago by ▴ 10
1
vote
18
replies
2.7k
views
Microarray expression analysis for on factor taking account confounders (covariables)
limma design matrix matrix with covariables
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
4
votes
17
replies
3.4k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma r differential gene expression
updated 7.7 years ago by 52k • written 7.7 years ago by ▴ 120
15
votes
17
replies
2.6k
views
Why p value inconsistent when using different number of pathway score?
limma
11 months ago • updated 10 months ago Chris ▴ 20
0
votes
17
replies
3.4k
views
Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.1 years ago by 52k • written 2.4 years ago by • 0
0
votes
17
replies
2.8k
views
Testing for no change in RNA-seq data?
limma limma
updated 12.0 years ago by ★ 3.8k • written 12.0 years ago by ★ 7.9k
0
votes
17
replies
2.4k
views
How to check linear model
modalmatrix limma R linear
2.1 years ago Jitendra ▴ 10
3
votes
17
replies
4.8k
views
filtering probes in affymetrix data
Annotation limma Annotation limma
updated 11.1 years ago by 68k • written 11.1 years ago by ▴ 180
3
votes
16
replies
4.6k
views
limma contrast matrix
limma contrast design and contrast matrix
10.4 years ago Smith H. ▴ 20
11
votes
16
replies
2.2k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 840
14
votes
16
replies
3.2k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 10
4
votes
16
replies
6.5k
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2 limma combat
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 10
14
votes
16
replies
3.4k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
8.8 years ago giroudpaul ▴ 40
7
votes
16
replies
6.2k
views
limma voom and trend
limma
updated 4.6 years ago by 52k • written 4.6 years ago by ▴ 20
3
votes
15
replies
3.2k
views
Are the p-values supposed to be on the order of 10^-120?
limma affy bioconductor affymetrix
updated 10.4 years ago by 52k • written 10.4 years ago by • 0
0
votes
15
replies
2.8k
views
Exon array annotation with limma?
Normalization limma biomaRt oneChannelGUI Normalization limma biomaRt oneChannelGUI
updated 15.3 years ago by ▴ 500 • written 15.3 years ago by ▴ 220
0
votes
15
replies
3.1k
views
PreFiltering probe in microarray analysis
Microarray limma oligo Microarray limma oligo
updated 13.8 years ago by ▴ 220 • written 13.8 years ago by ▴ 30
2
votes
15
replies
3.7k
views
limma: how to use pairing and adjust for covariates
limma limma-voom limma paired analysis limma contrast matrix
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
8
votes
15
replies
10k
views
Design matrix for continuous independent variable in limma
limma microarray
9.2 years ago Linda Chaba ▴ 10
4
votes
14
replies
6.1k
views
Including technical and biological replicates in Limma block analysis?
limma microarray block paired linear model
10.3 years ago vas ▴ 40
15
votes
14
replies
4.1k
views
extract similar expressed genes (SEGs) rather than DEGs
limma microarray
updated 10.1 years ago by 21k • written 10.2 years ago by ▴ 340
10
votes
14
replies
5.3k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 90
2
votes
14
replies
4.0k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma oligo annotation
updated 10.0 years ago by ▴ 130 • written 10.2 years ago by • 0
4
votes
14
replies
2.0k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 7 months ago by 52k • written 8 months ago by • 0
17
votes
14
replies
49k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 2.8 years ago by • 0 • written 7.7 years ago by ▴ 20
6
votes
14
replies
3.6k
views
Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 7.0 years ago by ▴ 840 • written 7.0 years ago by ▴ 30
8
votes
14
replies
3.4k
views
Batch with only one sample or condition
limma batch effect
updated 9.3 years ago by 52k • written 9.3 years ago by ▴ 70
6
votes
14
replies
2.7k
views
Help analyzing RNA-seq data from FPKM values with multiple time points
rnaseq limma
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
0
votes
14
replies
2.7k
views
Combining data from different versions of Illumina HumanHT-12 v3
probe limma ArrayExpress probe limma ArrayExpress
updated 14.0 years ago by ★ 3.6k • written 14.0 years ago by ▴ 220
6
votes
14
replies
3.6k
views
limma with continous covariate depending on gene, 2 block variables, pairing and technical replicates
limma covariate block paired samples technical replicates
updated 9.4 years ago by ★ 28k • written 9.4 years ago by ▴ 70
16
votes
13
replies
5.6k
views
Camera and ROAST
limma
updated 7.3 years ago by 52k • written 7.3 years ago by ▴ 30
2
votes
13
replies
2.6k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
7.1 years ago • updated 7.0 years ago SPbeginner • 0
2
votes
13
replies
2.3k
views
problem about (design matrix)
limma limma design matrix design matrix
updated 9.1 years ago by ★ 28k • written 9.1 years ago by • 0
0
votes
13
replies
2.9k
views
two color arrays normalization
limma limma
updated 16.1 years ago by ★ 2.0k • written 16.1 years ago by ▴ 110
0
votes
13
replies
3.1k
views
LIMMA decideTests result zero from contrast matrix
limma limma
12.9 years ago Ekta Jain ▴ 370
7
votes
13
replies
2.4k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 6.2 years ago by ★ 7.9k • written 6.2 years ago by ▴ 840
50 results • Page 1 of 1
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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
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