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The difference when using Limma compare between 3 conditions vs 2 conditions
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7 weeks ago • updated 20 days ago Chris ▴ 10
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Why p value inconsistent when using different number of pathway score?
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4 weeks ago • updated 18 days ago Chris ▴ 10
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SGSeq: moving toward diffex from SGSeq analysis
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Ensembl plants at annotationHub?
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updated 2 days ago by • 0 • written 5.5 years ago by ★ 4.0k
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
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written 14 days ago by • 0
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12
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6 months ago • updated 28 days ago shepherl 3.9k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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updated 20 days ago by • 0 • written 4.6 years ago by ▴ 10
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 18 days ago by 65k • written 2.4 years ago by • 0
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Log-cpm values from limma
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updated 10 days ago by 50k • written 4 weeks ago by • 0
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Limma design with continuous and categorical covariates
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updated 27 days ago by • 0 • written 7.8 years ago by ▴ 30
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Method to find pathways different between 2 groups
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14 days ago • updated 5 days ago Chris ▴ 10
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18 days ago shepherl 3.9k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
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updated 4 days ago by ★ 4.1k • written 5 days ago by • 0
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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17 days ago • updated 13 days ago gene_bioconductor ▴ 10
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Create protein sequences including variants from a VCF file
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updated 4 days ago by • 0 • written 5.2 years ago by ▴ 50
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475
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FilterByExpr low counts with small sample size
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4 weeks ago • updated 28 days ago Jonathan ▴ 10
4
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494
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Memory errors using read.bismark?
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5 weeks ago • updated 13 days ago Juan Higareda • 0
3
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4
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293
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Store output of matchPWM()
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19 days ago • updated 6 days ago mat149 ▴ 70
3
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3
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368
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permutation test in edgeR
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updated 29 days ago by 50k • written 6 weeks ago by • 0
3
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3
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253
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DESeq2 - dispersion estimation when there is none
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updated 27 days ago by 42k • written 28 days ago by • 0
3
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1
reply
329
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 26 days ago by 42k • written 26 days ago by ▴ 40
3
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1
reply
152
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How to save the DEXSeq results
DEXSeq
updated 14 days ago by 42k • written 14 days ago by • 0
3
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Cannabis and KEGGgraph
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updated 28 days ago by ★ 4.0k • written 4 weeks ago by ▴ 10
3
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3
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 21 days ago by ★ 4.1k • written 21 days ago by ▴ 10
3
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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?
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updated 12 days ago by 50k • written 5.6 years ago by ▴ 10
3
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5
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305
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Help with running egsea()
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13 days ago • updated 12 days ago Chris ▴ 10
3
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Extremely small p-values using Limma for proteomic data
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updated 10 days ago by 65k • written 13 days ago by • 0
3
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Help with error using camera() in limma
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20 days ago • updated 19 days ago Chris ▴ 10
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How to retrieve gene ontology GO class from gene list?
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updated 25 days ago by 65k • written 26 days ago by • 0
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398
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Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
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8 days ago • updated 3 days ago Matthew Thornton ▴ 360
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Trim/Filter out-of-bounds GRanges
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updated 14 days ago by 42k • written 14 days ago by ▴ 70
2
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3
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updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
2
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7
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411
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deseq2 results
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updated 14 days ago by 50k • written 16 days ago by ▴ 20
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minfi latest update for EPIC V2 chip
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updated 13 days ago by 65k • written 13 days ago by • 0
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EGSEA usage with microarray data (with vooma)?
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updated 11 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
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13
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Trying to use enrichGO
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28 days ago • updated 25 days ago fernanda.backsouza ▴ 10
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fgsea significant result
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15 days ago • updated 14 days ago Chris ▴ 10
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How to design DEXSeq formula for multiple variables
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updated 5 days ago by ★ 1.9k • written 7 days ago by • 0
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get BM error
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updated 26 days ago by 65k • written 26 days ago by • 0
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Error while installing BiocManager::install("org.Vdahliae.eg.db")
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5 days ago • updated 3 days ago Patadù ▴ 10
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updated 4 days ago by 50k • written 5 days ago by • 0
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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updated 24 days ago by 65k • written 25 days ago by • 0
2
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4
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Error EPICv2 ChAMP
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limma for gene expression analysis with big and unbalanced sample size
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updated 19 days ago by • 0 • written 8.0 years ago by • 0
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ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 6 days ago by • 0 • written 3.6 years ago by ▴ 60
2
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2
replies
286
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
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13 days ago • updated 7 days ago zzrammal • 0
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
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20 days ago Chris ▴ 10
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Answer: How to run allelic imbalance in apeglm by Michael Love 42k
You can put 1 / 1 for the ratio when you are missing counts and then set the weight for that matrix cell to 1e-6. Let me know if that's …
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Got you. Thanks again for your comments.
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