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2
votes
1
answer
68
views
1
answer
Limma DesignMatrix, dropping terms
limma designmatrix written 4 days ago by Keifa • 10 • updated 4 days ago by Aaron Lun • 20k
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1
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51
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1
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running GEO series matrix file normalization and DEGs in limma
normalization limma tutorial written 5 days ago by devarajsaranya • 0 • updated 5 days ago by James W. MacDonald ♦ 46k
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1
answer
53
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1
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venDiagram after limma showing more genes after specifying up or down regulated specifically
microarray limma venn diagram differential expression venndiagram written 8 days ago by A • 0 • updated 8 days ago by James W. MacDonald ♦ 46k
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52
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1
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Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
rnaseq limma edger written 9 days ago by Ahdee • 40 • updated 9 days ago by Gordon Smyth ♦ 34k
2
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1
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32
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1
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makeContrasts for comparing multiple levels of a factor variable to the reference level
limma makecontrasts diffrential expression written 12 days ago by S.Bamopoulos • 10 • updated 12 days ago by Gordon Smyth ♦ 34k
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1
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64
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1
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limma removeBatchEffect -- strange values in presence of NAs
limma removebatcheffect() written 13 days ago by jf1 • 0 • updated 13 days ago by Gordon Smyth ♦ 34k
2
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1
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80
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1
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Am I on the right tracks with a 3 factor design in Limma?
biobase limma R design matrix written 13 days ago by reubenmcgregor88 • 0 • updated 13 days ago by Gordon Smyth ♦ 34k
1
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1
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45
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1
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Repeated measurements wtih limma
limma limma design matrix written 15 days ago by Gurkenkönig • 0 • updated 15 days ago by Aaron Lun • 20k
2
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1
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58
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1
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Differential analysis between 2 groups (n=1) vs (n=3) moderated t-test
limma differential gene expression moderated t-test small sample size written 18 days ago by mrupji • 0 • updated 18 days ago by Gordon Smyth ♦ 34k
1
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1
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74
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1
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Problem with write.fit function
limma write.fit written 4 weeks ago by tillmann.ruland • 0 • updated 19 days ago by Adam Travis • 0
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1
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65
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1
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Deseq2 problem visualizing gene expression with batch corrected values
visualization limma deseq2 differential expression written 25 days ago by Mbosio85 • 0 • updated 22 days ago by Michael Love ♦ 18k
3
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1
answer
46
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1
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Using limma to model gene expression changes with age
limma linear model written 22 days ago by KCLiv • 0 • updated 22 days ago by Gordon Smyth ♦ 34k
4
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1
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67
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1
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[limma] Define contrasts for model with covariates
limma model.matrix makecontrasts written 23 days ago by enricoferrero • 570 • updated 23 days ago by Gordon Smyth ♦ 34k
2
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1
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66
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1
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Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
limma limma design matrix confounders limma-voom written 23 days ago by S.Bamopoulos • 10 • updated 23 days ago by Aaron Lun • 20k
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3
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3
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LIMMA on RT-PCR data
limma pcr written 4.7 years ago by Sandhya Pemmasani Kiran • 40 • updated 24 days ago by Gordon Smyth ♦ 34k
3
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1
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75
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1
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edgeR: setting up proper contrasts for interactions
limma edger written 26 days ago by fcamus • 0 • updated 26 days ago by Aaron Lun • 20k
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1
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37
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1
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Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
limma lumi illumina gene expression data written 26 days ago by hks04180 • 0 • updated 26 days ago by Gordon Smyth ♦ 34k
1
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1
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50
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1
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ANOVA in ROAST
limma written 28 days ago by chris86 • 380 • updated 28 days ago by Gordon Smyth ♦ 34k
1
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1
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71
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1
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How to extract gene clusters (genes of similar pattern over time) once spline curves are fitted?
limma voom spline time course experiment gene cluster written 5 weeks ago by h.valipour.k • 0 • updated 4 weeks ago by Gordon Smyth ♦ 34k
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1
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75
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1
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Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent file of GEO data or how to makethe expression matrix step by step from GEO raw data (Agilent array data)
microarray limma geo agilent microarrays written 5 weeks ago by hks04180 • 0 • updated 5 weeks ago by James W. MacDonald ♦ 46k
0
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1
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91
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1
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Removing batch effect from gene expression before Limma linear modelling
limma differential gene expression covariates batch effect correction written 5 weeks ago by abelsousa • 0 • updated 5 weeks ago by Gordon Smyth ♦ 34k
2
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2
answers
108
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2
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The error when using beadarry and limma packages for analysing illumina chip
limma beadarray illumina written 5 weeks ago by 261092095 • 0 • updated 5 weeks ago by Gordon Smyth ♦ 34k
1
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1
answer
55
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1
answer
topTable error: data.frame(logFC = M[top]) : row names contain missing values
limma written 6 weeks ago by owen.whitley • 0 • updated 6 weeks ago by Aaron Lun • 20k
0
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1
answer
64
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1
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Getting Significance for second factor (bioreplicate/subject) when using limma.
limma anova written 6 weeks ago by wewolski • 10 • updated 6 weeks ago by Aaron Lun • 20k
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0
answers
68
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0
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Normalize a gene using lib size from another matrix
limma written 6 weeks ago by R • 40
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