Showing : Limma • reset
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Time course experiment using limma
limma Multi-levelExperiments Microarray
3.6 years ago Wendy ▴ 10
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4
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2.0k
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How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
3.6 years ago mohammedtoufiq91 ▴ 10
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2
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1.9k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
3.6 years ago fluentin44 • 0
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6
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3.1k
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Differential expression analysis - Clariom S array -workflow
design-matrix limma
3.6 years ago ala • 0
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1
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1.9k
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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 3.6 years ago by 53k • written 16.7 years ago by ▴ 30
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1.2k
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
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1.6k
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lncRNA Differential Expression Analysis
DESeq2 limma RNASeqData
3.6 years ago sushimoto • 0
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3
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1.4k
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how to change axis labeling in limma density plot
desnity limma
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 40
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4
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1.4k
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How to model a pre and post treatment in limma
limma
3.6 years ago AST ▴ 60
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8
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2.7k
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Limma : time course experiment with missing data
limma limma-voom
updated 2.6 years ago by • 0 • written 7.7 years ago by • 0
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4
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1.2k
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limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq limma
3.6 years ago danphillips28 ▴ 10
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826
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Differences between limma and edgeR
limma
3.7 years ago • updated 3.6 years ago jose.carmeliet • 0
6
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2
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968
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The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 30
4
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4
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1.2k
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Covariates to be included in DE model
DESeq2 limma
updated 2.8 years ago by 43k • written 3.7 years ago by • 0
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9
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5.4k
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Handling of missing values in limma
limma missingValues
updated 3.5 years ago by 53k • written 3.7 years ago by ▴ 10
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Limma interaction term
RNASeqData limma DifferentialExpression
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
2
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2
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1.8k
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Complex contrasts in limma
RNASeq limma DifferentialExpression
3.7 years ago tcalvo ▴ 100
2
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6
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4.0k
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how plotSA shall look like for good or bad data, any example of good or bad data shall look like in plotSA regarding whether the data is OK for limma…
plotSA limma
3.7 years ago Ming ▴ 380
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3
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2.1k
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limma voom contrasts
contrasts limma voom
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 90
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3
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Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
3.7 years ago nhaus ▴ 70
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3
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1.5k
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Need help with a contrast design for limma with a missing group?
limma VOOM
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 60
2
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1
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1.2k
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DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
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1
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2.1k
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How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.7 years ago by ★ 5.0k • written 3.7 years ago by ▴ 70
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1
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1.5k
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Running limma in parallel
parallel R limma EWAS
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
3
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6
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12k
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Unable to install "limma" package on RStudio
Bioconductor limma limmaGUI
3.7 years ago jaydengitt • 0
4
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5
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2.4k
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What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 3.5 years ago by • 0 • written 3.7 years ago by ▴ 70
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5
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1.9k
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Where to find old limma packages not part of a Bioc release?
archive limma
3.7 years ago Jonathan • 0
0
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1
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850
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How to design limma for two populations from each tumor, multiple tumors from several of the patients
limma
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
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2
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
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4
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2.3k
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How do you get averages of each group in Limma output
RNASeq limma
3.8 years ago Matthew • 0
4
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3
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1.7k
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Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
3
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4
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Phosphoproteomics time series analysis with splines
limma splines
3.9 years ago • updated 3.8 years ago rina ▴ 30
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2.3k
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Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric
limma
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
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825
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
3.9 years ago Jonas • 0
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2
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5.1k
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EdgeR installation issue
limma edgeR DESeq2
3.9 years ago aonghus • 0
2
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5
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2.6k
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Adjust for base line gene expression in limma model
limma Microarray
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
3
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2.2k
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Filtering low coverage RRBS counts results in few reads. Any alternatives?
limma edgeR
updated 3.9 years ago by ▴ 10 • written 3.9 years ago by • 0
3
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5
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limma-trend and voom results do not agree
limma limma-trend voom RNASeq
4.0 years ago • updated 3.9 years ago Tyler Sagendorf ▴ 10
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962
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limma KNN classification with voom-transformed data
limma KNN
updated 3.9 years ago by ★ 13k • written 3.9 years ago by • 0
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interpretation complex design limma
limma
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
3
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2
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2.3k
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Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 12 months ago by 53k • written 4.0 years ago by • 0
0
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7
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4.5k
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using limma package for paired t-test: Error: (subscript) logical subscript too long
limma limma
written 13.8 years ago by ▴ 580
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3
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2.2k
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Aggregating genes from multiple GSE's, ranking them, then building a PPI network.
GEOquery CancerData limma RCy3 CancerInSilico
updated 4.0 years ago by ★ 13k • written 4.0 years ago by ▴ 50
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Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
4.0 years ago svlachavas ▴ 840
2
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5
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2.0k
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Extracting fitted expression in limma
limma
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
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4.4k
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Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 21 months ago by • 0 • written 4.0 years ago by ▴ 380
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Advice to use block factor and duplicatecorrelation in RNA-seq experiment
limma
4.0 years ago jfertaj ▴ 30
2
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4
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2.0k
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DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2 limma modelmatrix edgeR designmatrix
updated 4.0 years ago by 53k • written 4.1 years ago by • 0
1
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2
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1.1k
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Unequal sample pools
limma pooling
4.1 years ago Jenny G • 0
0
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0
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1.2k
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SVAseq for differential transcript usage and differential splicing analysis
limma sva Leafcutter SVAseq
4.1 years ago georgia.katsoula ▴ 40
4,225 results • Page 8 of 85
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
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Popular Question to edward.esiribloom • 0
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