Showing : LIMMA • reset
5
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 14 days ago by • 0 • written 7.7 years ago by ▴ 30
15
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23
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2.0k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 7 days ago Chris • 0
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3
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1.5k
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 7 days ago by • 0 • written 13.0 years ago by ▴ 10
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1
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1.5k
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Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 2 hours ago by 50k • written 5.6 years ago by ▴ 10
5
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9
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1.3k
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Batch correction and repeated measures
RUVSeq sva limma
updated 20 days ago by 50k • written 7 months ago by ▴ 10
14
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17
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1.2k
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Why p value inconsistent when using different number of pathway score?
limma
17 days ago • updated 6 days ago Chris • 0
2
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2
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1.1k
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 7 days ago by • 0 • written 7.9 years ago by • 0
5
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9
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932
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Light difference when using coef vs omit a group when compare 3 groups.
limma
27 days ago • updated 19 days ago Chris • 0
0
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4
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603
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 days ago by 42k • written 6 months ago by • 0
2
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6
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409
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
29 days ago Chris • 0
1
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3
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352
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 22 days ago by 50k • written 27 days ago by • 0
1
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2
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338
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 4 days ago by 50k • written 4 days ago by • 0
0
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7
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
20 days ago • updated 14 days ago hortense96 • 0
0
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3
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246
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 7 days ago by 65k • written 8 days ago by • 0
3
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4
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221
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Help with error using camera() in limma
CAMERA limma
7 days ago Chris • 0
0
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2
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215
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
18 days ago • updated 15 days ago catv • 0
3
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1
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179
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Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
0
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2
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170
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 15 days ago by • 0
0
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1
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109
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Gene-by-sample covariates in limma
Metabolomics limma
updated 5 days ago by 50k • written 5 days ago by • 0
1
vote
1
reply
66
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
updated 12 hours ago by 65k • written 13 hours ago by • 0
1
vote
1
reply
56
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 13 hours ago by 65k • written 14 hours ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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