Showing : limma • reset
5
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10
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186
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How to do annotation with Limma
annotation limma
updated 1 day ago by ★ 3.0k • written 5 days ago by • 0
2
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3
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96
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RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 4 days ago by • 0 • written 8 days ago by • 0
3
votes
4
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194
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Combining repeated measurements and duplicateCorrelation in LIMMA
limma
updated 7 days ago by 57k • written 10 days ago by ▴ 20
3
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3
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100
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Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 7 days ago by 57k • written 8 days ago by • 0
0
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3
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105
views
[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma edgeR DEseq2
updated 9 days ago by 33k • written 9 days ago by ▴ 10
0
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0
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39
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Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi limma lmm lmfit dmpFinder
20 days ago • updated 19 days ago kyleyxw • 0
0
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0
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51
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Use limma to a non-genomic data
non-genomic quantitative limma
24 days ago Marcelo Laia ▴ 440
1
vote
3
replies
117
views
The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
2
votes
2
replies
108
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
4 weeks ago tjbencomo • 0
1
vote
1
reply
117
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 4 weeks ago by 3.1k • written 5 weeks ago by • 0
0
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0
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65
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Crossover with repeated measures
limma
5 weeks ago ijvechetti • 0
1
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2
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126
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limma - removing samples?
ArrayExpress limma arrays
5 weeks ago RMP87 • 0
0
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3
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135
views
Limma paired analysis design question
limma
updated 5 weeks ago by 43k • written 6 weeks ago by ▴ 20
1
vote
0
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80
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
7 weeks ago Junghoon ▴ 10
0
votes
1
reply
129
views
Error while running variancePartition::dream()
variancePartition limma BiocParallel
7 weeks ago Junghoon ▴ 10
0
votes
1
reply
109
views
Excessive memory requirement of variancePartition::dream()
variancePartition limma BiocParallel
7 weeks ago • updated 6 weeks ago Junghoon ▴ 10
0
votes
12
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342
views
How to estimate prediction variance for limma mixed-effects models
limma
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 20
0
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1
reply
500
views
model.matrix question
limma limma
updated 7 weeks ago by 43k • written 13.0 years ago by ▴ 90
0
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6
replies
197
views
Sample quality weights for RNA-seq
DESeq2 limma weight
9 weeks ago • updated 8 weeks ago Naomi Altman ★ 6.0k
4
votes
2
replies
139
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 9 weeks ago by 57k • written 9 weeks ago by • 0
0
votes
1
reply
103
views
Query regarding edgeR and limma
limma readDGE edgeR
updated 9 weeks ago by 57k • written 9 weeks ago by • 0
0
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4
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181
views
Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
9 weeks ago Nirad • 0
0
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2
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138
views
Limma experiment design and making contrasts
limma methylationArrayAnalysis
9 weeks ago Kesava • 0
1
vote
2
replies
214
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 10 weeks ago by 43k • written 12 weeks ago by ▴ 10
0
votes
1
reply
143
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
1
vote
2
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143
views
How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
11 weeks ago • updated 7 weeks ago a.deb • 0
0
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2
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141
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
11 weeks ago annadv • 0
0
votes
4
replies
200
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
updated 11 weeks ago by ▴ 270 • written 11 weeks ago by ▴ 10
3
votes
2
replies
173
views
Multi-level comparisons with paired data: duplicateCorrelation or not?
limma
12 weeks ago • updated 11 weeks ago Lluís Revilla Sancho ▴ 640
1
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7
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283
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how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3 months ago decppced • 0
0
votes
11
replies
356
views
Hello, I'm having trouble in installing Limma package and this is what Im getting
limma
updated 12 weeks ago by 3.1k • written 3 months ago by • 0
6
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4
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260
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Discrepancy in effect size calculation between ordinary Cohens D and LIMMA
CohensD power limma effectsize
3 months ago • updated 12 weeks ago MoltenLight ▴ 10
4
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3
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218
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 12 weeks ago by 43k • written 3 months ago by ▴ 10
0
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1
reply
109
views
Is there is any distribution assumption for voom tranformed matrix?
limma
updated 3 months ago by 43k • written 3 months ago by • 0
5
votes
6
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305
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 3 months ago by 43k • written 3 months ago by ▴ 10
3
votes
3
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201
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
3 months ago Federico Alessandro • 0
0
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0
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96
views
Limma design multi-level experiment with 3 time points
R proteomics limma
3 months ago ellen2270 • 0
0
votes
1
reply
102
views
possible problem with mzR? cannot load Msnset for proteomics analysis
MSnbase mzR Bioconductor limma
updated 3 months ago by 1.5k • written 3 months ago by • 0
0
votes
3
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174
views
add group info within DGE-object before TMM normalization
edgeR limma
updated 3 months ago by 43k • written 3 months ago by ▴ 40
0
votes
3
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166
views
How to calculate coefficient of variation within group?
edgeR limma RNASeqPower
updated 3 months ago by 43k • written 3 months ago by ▴ 50
2
votes
3
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169
views
ANOVA Limma
ANOVA limma
updated 3 months ago by 57k • written 3 months ago by ▴ 10
0
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2
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164
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3 months ago RJM • 0
3
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7
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292
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3 months ago by 43k • written 3 months ago by ▴ 20
5
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4
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216
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4 months ago snijesh • 0
0
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0
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89
views
limma on RNASeq time-series with patient and batch as blocking factor
duplicateCorrelation limma BatchEffect
4 months ago Julia • 0
1
vote
2
replies
174
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4 months ago Dan ▴ 10
3
votes
9
replies
290
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
4 months ago Daniel.Schnell • 0
1
vote
1
reply
129
views
Creating a design matrix
limma
updated 4 months ago by 57k • written 4 months ago by • 0
3
votes
3
replies
261
views
Using limma for the analysis of qPCR data
NormqPCR EasyqpcR qPCR HTqPCR limma
updated 4 months ago by 43k • written 4 months ago by ▴ 570
0
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0
replies
216
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4 months ago Papyrus ▴ 10
50 results • Page 1 of 1
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Comment: Data input for aracne2regulon function in viper package by Luna_P • 0
Hello Keith, I am currently trying to use my ARACNE-AP generated networks in Viper. I did all three steps you mentioned above but my prob…
Answer: DESeq2 for allele-specific expression with contrasts between conditions by Michael Love 33k
There is a section in the vignette on interactions that will help you here. You want to test for within-individual effects (`allele`) and c…
Answer: Issues with Tximport by Michael Love 33k
Your file has no version numbers, while your `tx2gene` does have version numbers. While the names look similar, they are not a match. tximp…
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w by Michael Love 33k
This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.
Comment: DESeq2: NA's in mcols(object)$betaConv by Michael Love 33k
They are actually rounded to zero in the `dds` which requires integer values.
Votes
Comment: DESeq2: NA's in mcols(object)$betaConv
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: RUVSeq and Salmon
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