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The difference when using Limma compare between 3 conditions vs 2 conditions
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7 weeks ago • updated 18 days ago Chris ▴ 10
15
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17
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Why p value inconsistent when using different number of pathway score?
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28 days ago • updated 17 days ago Chris ▴ 10
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SGSeq: moving toward diffex from SGSeq analysis
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updated 2 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
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Ensembl plants at annotationHub?
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updated 1 day ago by • 0 • written 5.5 years ago by ★ 4.0k
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19
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 18 days ago by • 0 • written 4.6 years ago by ▴ 10
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
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Estimating Cell Counts for EPIC V2 array data
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written 11 weeks ago by • 0
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Which input file is used for DGEList in EgdeR?
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updated 29 days ago by • 0 • written 15 months ago by ▴ 10
5
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Log-cpm values from limma
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updated 8 days ago by 50k • written 4 weeks ago by • 0
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updated 25 days ago by • 0 • written 7.8 years ago by ▴ 30
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 16 days ago by 65k • written 2.3 years ago by • 0
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9
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Create protein sequences including variants from a VCF file
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updated 3 days ago by • 0 • written 5.2 years ago by ▴ 50
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491
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Memory errors using read.bismark?
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5 weeks ago • updated 11 days ago Juan Higareda • 0
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2
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624
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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16 days ago • updated 12 days ago gene_bioconductor ▴ 10
4
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Method to find pathways different between 2 groups
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13 days ago • updated 3 days ago Chris ▴ 10
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News: Bioconductor 3.19 is Released!
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17 days ago shepherl 3.9k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
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updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
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6
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469
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FilterByExpr low counts with small sample size
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4 weeks ago • updated 26 days ago Jonathan ▴ 10
3
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3
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368
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permutation test in edgeR
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updated 27 days ago by 50k • written 5 weeks ago by • 0
3
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1
reply
148
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How to save the DEXSeq results
DEXSeq
updated 12 days ago by 42k • written 12 days ago by • 0
3
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Help with running egsea()
EGSEA
12 days ago • updated 11 days ago Chris ▴ 10
3
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1
reply
328
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 25 days ago by 42k • written 25 days ago by ▴ 40
3
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1
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Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 11 days ago by 50k • written 5.6 years ago by ▴ 10
3
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4
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276
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Store output of matchPWM()
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17 days ago • updated 5 days ago mat149 ▴ 70
3
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2
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Cannabis and KEGGgraph
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updated 26 days ago by ★ 4.0k • written 29 days 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 19 days ago by ★ 4.1k • written 19 days ago by ▴ 10
3
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1
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Job: Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job Job machine learning deep learning computational biology
written 6.3 years ago by ▴ 180
3
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3
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251
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 25 days ago by 42k • written 26 days ago by • 0
3
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10
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453
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Extremely small p-values using Limma for proteomic data
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updated 8 days ago by 65k • written 11 days ago by • 0
3
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4
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262
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Help with error using camera() in limma
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18 days ago Chris ▴ 10
3
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4
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517
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 10 days ago by ★ 6.5k • written 13 days ago by • 0
2
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1
reply
143
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Trim/Filter out-of-bounds GRanges
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updated 12 days ago by 42k • written 12 days ago by ▴ 70
2
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3
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254
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Too many significant genes when integrating gtex and tcga
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updated 13 days ago by ★ 4.1k • written 15 days ago by • 0
2
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235
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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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19 days ago Chris ▴ 10
2
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7
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381
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deseq2 results
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10 days ago • updated 7 days ago sajadahmad41454 • 0
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2
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228
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fgsea significant result
fgsea
14 days ago • updated 13 days ago Chris ▴ 10
2
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3
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269
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package goseq seems to be not available on the latest version of R
goseq
updated 12 days ago by 50k • written 15 days ago by ▴ 20
2
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3
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ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 5 days ago by • 0 • written 3.6 years ago by ▴ 60
2
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13
replies
481
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Trying to use enrichGO
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27 days ago • updated 24 days ago fernanda.backsouza ▴ 10
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Problem installing ChAMP on a MacBook
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updated 2 days ago by 3.9k • written 2 days ago by • 0
2
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3
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119
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 3 days ago by 50k • written 3 days ago by • 0
2
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limma for gene expression analysis with big and unbalanced sample size
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updated 18 days ago by • 0 • written 8.0 years ago by • 0
2
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2
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217
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OrgDb for maize
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updated 29 days ago by 65k • written 4 weeks ago by • 0
2
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5
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307
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get BM error
ensembldb
updated 24 days ago by 65k • written 24 days ago by • 0
2
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1
reply
170
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minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 11 days ago by 65k • written 11 days ago by • 0
2
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9
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427
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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updated 23 days ago by 65k • written 23 days ago by • 0
2
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1
reply
69
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How to design DEXSeq formula for multiple variables
DEXSeq
updated 3 days ago by ★ 1.9k • written 5 days ago by • 0
2
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4
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284
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Error EPICv2 ChAMP
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updated 26 days ago by 65k • written 4 weeks ago by • 0
2
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5
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DESeq2 setting significant p-value
DESeq2
updated 29 days ago by 42k • written 5.0 years ago by ▴ 10
2
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5
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258
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 23 days ago by 65k • written 25 days ago by • 0
177 results • Page 1 of 4
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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