15
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23
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2.1k
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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
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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4 weeks ago • updated 19 days ago Chris ▴ 10
10
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10
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
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39
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Ensembl plants at annotationHub?
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updated 3 days ago by • 0 • written 5.5 years ago by ★ 4.0k
7
votes
6
replies
622
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
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written 15 days ago by • 0
6
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12
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
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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 20 days ago by • 0 • written 4.6 years ago by ▴ 10
5
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6
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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
5
votes
8
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8.9k
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Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 27 days ago by • 0 • written 7.8 years ago by ▴ 30
5
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3
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319
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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
4
votes
9
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3.1k
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Create protein sequences including variants from a VCF file
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updated 5 days ago by • 0 • written 5.2 years ago by ▴ 50
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5
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338
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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
4
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6
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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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2
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634
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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18 days ago • updated 14 days ago gene_bioconductor ▴ 10
4
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9
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272
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 4 days ago by ★ 4.1k • written 5 days ago by • 0
4
votes
9
replies
494
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Memory errors using read.bismark?
dmrseq bsseq
5 weeks ago • updated 13 days ago Juan Higareda • 0
4
votes
0
replies
147
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News: Bioconductor 3.19 is Released!
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19 days ago shepherl 3.9k
3
votes
4
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266
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Help with error using camera() in limma
CAMERA limma
20 days ago Chris ▴ 10
3
votes
3
replies
253
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 27 days ago by 42k • written 28 days ago by • 0
3
votes
3
replies
274
views
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
votes
1
reply
329
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 26 days ago by 42k • written 27 days ago by ▴ 40
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 12 days ago by 50k • written 5.6 years ago by ▴ 10
3
votes
1
reply
153
views
How to save the DEXSeq results
DEXSeq
updated 14 days ago by 42k • written 14 days ago by • 0
3
votes
4
replies
293
views
Store output of matchPWM()
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19 days ago • updated 7 days ago mat149 ▴ 70
3
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3
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370
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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
votes
5
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305
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Help with running egsea()
EGSEA
14 days ago • updated 12 days ago Chris ▴ 10
3
votes
10
replies
488
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 65k • written 13 days ago by • 0
3
votes
2
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238
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Cannabis and KEGGgraph
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updated 28 days ago by ★ 4.0k • written 4 weeks ago by ▴ 10
2
votes
5
replies
262
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 25 days ago by 65k • written 27 days ago by • 0
2
votes
2
replies
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…
RCy3
9 days ago • updated 4 days ago Matthew Thornton ▴ 360
2
votes
3
replies
279
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package goseq seems to be not available on the latest version of R
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updated 14 days ago by 50k • written 17 days ago by ▴ 20
2
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1
reply
148
views
Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 14 days ago by 42k • written 14 days ago by ▴ 70
2
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7
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417
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deseq2 results
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12 days ago • updated 9 days ago sajadahmad41454 • 0
2
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4
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167
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DESeq2- Mysterious interaction suppresses DEGs
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updated 7 hours ago by 42k • written 3 days ago by • 0
2
votes
2
replies
233
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fgsea significant result
fgsea
16 days ago • updated 15 days ago Chris ▴ 10
2
votes
2
replies
239
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago Chris ▴ 10
2
votes
3
replies
120
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Problem installing ChAMP on a MacBook
ChAMP
updated 4 days ago by 3.9k • written 4 days ago by • 0
2
votes
1
reply
186
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minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 13 days ago by 65k • written 13 days ago by • 0
2
votes
3
replies
258
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 15 days ago by ★ 4.1k • written 17 days ago by • 0
2
votes
2
replies
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 20 days ago by • 0 • written 8.0 years ago by • 0
2
votes
1
reply
85
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 5 days ago by ★ 1.9k • written 7 days ago by • 0
2
votes
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
limma
13 days ago • updated 7 days ago zzrammal • 0
2
votes
3
replies
140
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 5 days ago by 50k • written 5 days ago by • 0
2
votes
5
replies
224
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
5 days ago • updated 3 days ago Patadù ▴ 10
2
votes
13
replies
493
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
29 days ago • updated 26 days ago fernanda.backsouza ▴ 10
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 7 days ago by • 0 • written 3.6 years ago by ▴ 60
2
votes
4
replies
290
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 28 days ago by 65k • written 4 weeks ago by • 0
2
votes
5
replies
315
views
get BM error
ensembldb
updated 26 days ago by 65k • written 26 days ago by • 0
2
votes
9
replies
428
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 25 days ago by 65k • written 25 days ago by • 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
updated 12 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
172 results • Page 1 of 4
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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