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How to use limma for a categorial outcome variable? Where outcome is the cohort status and predictor is gene expression.
next-gen rna limma rna-seq written 21 days ago by halo22 • 120 • updated 1 hour ago by Biostar ♦♦ 20
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Do we need to filter out control probes and low expressed probes (as given in LIMMA user guide 2016 page number 111) for all Agilent microarray platform
agilent microarray limma written 9 days ago by anandprem1792 • 0
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Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
confounding limma rna-seq voom written 10 months ago by stefanos.bamopoulos • 30 • updated 10 days ago by Gordon Smyth • 750
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Is fold change of value 1.5 (log2FC = 0.58) a significant value ?
agilent limma microarray analysis written 11 days ago by anandprem1792 • 0 • updated 11 days ago by WouterDeCoster ♦ 38k
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Experimental design RNAseq differential expression
rna-seq edger limma differential expression batch written 28 days ago by Pietro • 50 • updated 19 days ago by Biostar ♦♦ 20
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Model selection for differential expression
methylation limma rna-seq differential expression written 23 days ago by rmf • 560
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differential gene set testing combining genes from multiple panels
pathway limma rna-seq voom written 29 days ago by glocke01 • 160 • updated 29 days ago by Gordon Smyth • 750
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Microarray analysis in R (Limma): how to select genes exclusively expressed in one condition.
R microarray limma written 5 weeks ago by reubenmcgregor88 • 40 • updated 5 weeks ago by h.mon ♦ 24k
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removeBatchEffect with or without log2 values
removebatcheffect R limma written 7 weeks ago by hesse.sebastian • 80
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How to correctly correct for batch effects
removebatcheffect R pvca limma written 7 weeks ago by hesse.sebastian • 80
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error in read.maimages {limma}
microarray limma written 7 weeks ago by 594915965 • 0 • updated 7 weeks ago by Gordon Smyth • 750
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Gene set analysis - minimum number of genes for moderated t statistics
gene set analysis moderated t statistics limma written 11 weeks ago by SB • 0 • updated 9 weeks ago by Gordon Smyth • 750
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5 follow
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Limma can make differential expression with just one case in one group?
differential expression limma rna-seq written 11 weeks ago by ra2967 • 10 • updated 10 weeks ago by Gordon Smyth • 750
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Differential expressed genes for GRN
grn limma rna-seq written 10 weeks ago by marwwa11 • 0 • updated 10 weeks ago by Kevin Blighe ♦ 41k
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LIMMA analysis with 2 samples in comparison group
proteomics R limma written 3 months ago by hesse.sebastian • 80
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Design matrix for voom: with or without batch blocking?
proteomics R limma voom written 3 months ago by hesse.sebastian • 80 • updated 3 months ago by i.sudbery ♦ 4.3k
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Same Values In Limma/Microarray Differential Expression
microarray limma output differential expression written 3 months ago by Wan Fahmi • 0 • updated 3 months ago by RamRS ♦ 21k
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Normalize and filter RNA-seq data
limma rna-seq written 3 months ago by Phoenix Mu • 0
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How to deal with large inter-sample variation when using GTEx RNA-seq data?
variation deseq2 rna-seq gtex limma written 4 months ago by Akos • 20
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A question about how the kegga function or KEGG analysis in general determines significance.
kegga rna-seq kegg edger limma written 4 months ago by brett.vanderwerff • 20
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combine shRNA-Seq on gene level
ngs shrna-seq limma roast written 4 months ago by Assa Yeroslaviz • 1.2k
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5 follow
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Normalization for small non-coding RNA (piRNAs)
normalization deseq2 limma edger written 4 months ago by Konstantinos Yeles • 40 • updated 4 months ago by A. Domingues • 2.0k
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How to eliminate batch effect using removeBatchEffect function for tissue expression profiles?
R batch-effect microarray limma written 5 months ago by rice.researcher • 130 • updated 5 months ago by zx8754 ♦ 7.1k
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RNA seq help: limma remove batch effect without full rank design
R batch-effect limma rna-seq written 6 months ago by jhasselm • 0 • updated 5 months ago by zx8754 ♦ 7.1k
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RTqPCR Differential Expression with multivariate linnear models
R limma linnear model written 5 months ago by v82masae • 120 • updated 5 months ago by Kevin Blighe ♦ 41k
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Remove lines from a toptable that have an empty ID (symbol)
gene R toptable limma written 5 months ago by mannoulag1 • 60 • updated 5 months ago by zx8754 ♦ 7.1k
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18 follow
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How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene limma edger written 17 months ago by Mike • 1.3k • updated 5 months ago by enxxx23 • 210
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Batch effect correction in DE analysis of single cell RNA-seq data and visualization
scde batch effect limma seurat rna-seq written 5 months ago by Poorya Parvizi • 40 • updated 5 months ago by Praneet Chaturvedi • 110
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EnhancedVolcano with gene names
R enhancedvolcano limma written 6 months ago by mannoulag1 • 60
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designing loop for my Linear model function
array limma rna-seq written 6 months ago by rida.rehman • 0 • updated 6 months ago by genomax ♦ 65k
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