0
votes
2
replies
1.3k
views
org.Hs.eg.db - Error in mapping gene symbol to gene id?
org.hs.eg.db annotation error
updated 9.5 years ago by 68k • written 9.5 years ago by • 0
2
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2
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1.8k
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limma roast/mroast with patient-matched pre-/post- treatment
limma roast mroast block
updated 9.5 years ago by ★ 7.9k • written 9.5 years ago by • 0
0
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4
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Is it possible to install previous versions of the packages instead of the newest ones?
bioconductor
written 9.5 years ago by • 0
0
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1
reply
1.2k
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Mapping sequence features to alignments
pairwisealignment indel
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 10
11
votes
3
replies
6.5k
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WGCNA - Signed vs signed hybrid networks
wgcna
updated 9.5 years ago by ★ 3.0k • written 9.5 years ago by ▴ 20
2
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1
reply
1.6k
views
Warnings messages can not we handles/hidden
warning message warning R rhdf5
updated 9.5 years ago by 25k • written 9.6 years ago by • 0
11
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7
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8.7k
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What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 9.5 years ago by ★ 7.9k • written 9.5 years ago by ▴ 70
1
vote
2
replies
1.7k
views
Expand annotation on a vcf file
vcf variantannotation
updated 9.5 years ago by ★ 11k • written 9.5 years ago by • 0
1
vote
10
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2.9k
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UCSC web service API
txdb.hsapiens.ucsc.hg19.knowngene rtracklayer
updated 9.5 years ago by 25k • written 9.5 years ago by ▴ 290
2
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2
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5.3k
views
Bgratio column in clusterProfiler enrichGO results
clusterprofiler
updated 2.5 years ago by • 0 • written 9.5 years ago by ▴ 10
1
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1
reply
2.5k
views
News: New Master of Science in Quantitative and Computational Biology at University of Trento, Italy
computational biology bioinformatics teaching master News
updated 9.5 years ago by • 0 • written 9.6 years ago by ▴ 10
1
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2
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1.5k
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motifMatrix input object type, confused VRange and GRange
somaticsignatures
updated 9.5 years ago by ★ 1.3k • written 9.5 years ago by ▴ 10
6
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4
replies
5.1k
views
RSEM expected counts to limma-voom
limma voom rsem
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 90
1
vote
1
reply
1.4k
views
Generating ExpressionSet Objects
r expressionset subseq rnaseq
updated 9.5 years ago by 25k • written 9.5 years ago by ▴ 70
0
votes
7
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4.0k
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Repeated Measures mRNA expression analysis II
limma edgeR DESeq
updated 9.5 years ago by • 0 • written 12.6 years ago by ▴ 140
0
votes
4
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2.0k
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Error in GOFrame due to NA for unsupported organism (Gene Ontology)
reportingtools annotationhub gostats
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 20
0
votes
1
reply
998
views
Clearing predefined values in variables
variables
9.5 years ago humberto_munoz • 0
1
vote
2
replies
3.1k
views
troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 9.5 years ago by 16k • written 9.5 years ago by ★ 4.1k
9
votes
7
replies
3.7k
views
News: Conference: BioC 2016: Where Software and Biology Connect, Stanford, 24-26 June
BioC2016 Conference News
updated 9.5 years ago by 4.3k • written 10.0 years ago by 25k
0
votes
2
replies
917
views
limma multi level experiment
limma
updated 9.5 years ago by ★ 7.9k • written 9.5 years ago by ▴ 10
4
votes
3
replies
2.7k
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Analyzing microbiome data (many zero-counts) using DESeq2
DESeq2 microbiome zero-inflated
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
1
vote
2
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3.0k
views
Installation Error- GO.db
GO.db
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 10
1
vote
1
reply
1.4k
views
affyPLM boxplots for subset of samples
affyPLM
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 360
0
votes
0
replies
1.1k
views
Package to study genetic interactions for a continuous phenotype
genetic epidemiology
9.5 years ago p1990 • 0
0
votes
7
replies
2.3k
views
PCA results different from th same sample but different counting method
deseq2 pca tximportdata htseqcounts
updated 9.5 years ago by 43k • written 9.5 years ago by ▴ 40
0
votes
5
replies
924
views
Why does rmoving features with low sequence counts influence the Wald statistic and fold change values in the DESeq2 output?
deseq2
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
0
votes
1
reply
1.6k
views
why my resultsNames(deseq) is not the same as model.matrix ?
deseq2 RNASeq SVA
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
3
votes
5
replies
2.4k
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How can I coerce "list" to S4 "List" (reproducible example is available)?
coercion data manipulation s4vectors List
9.5 years ago Jurat Shahidin ▴ 80
3
votes
7
replies
3.3k
views
ChIPQC for a single sample (disabling facets)
ChipQc chipqc
9.5 years ago Coby Viner ▴ 50
0
votes
0
replies
1.3k
views
GAGE package statistical tests
t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment
9.5 years ago smt8n • 0
3
votes
8
replies
2.7k
views
Vcf to VRanges conversion error: ["incorrect number of dimensions"]
variantannotation somaticsignatures
updated 9.5 years ago by ★ 11k • written 9.5 years ago by • 0
2
votes
1
reply
763
views
illuminaHumanv4.db versus illuminaHumanv2.db beadchip annotation differences
limma microarray
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 420
1
vote
1
reply
1.1k
views
CGEN package, how to set main and interacting variables
cgen
updated 9.5 years ago by ▴ 10 • written 9.5 years ago by • 0
0
votes
14
replies
4.6k
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Error in ReactomePA
r reactomepa
updated 9.5 years ago by ★ 1.2k • written 9.5 years ago by ▴ 20
0
votes
2
replies
2.8k
views
ANOTA: anotaPerformQc results in quantile error
anota
updated 9.5 years ago by • 0 • written 10.5 years ago by • 0
1
vote
15
replies
3.4k
views
DMRcate results meanpvals
dmrcate
updated 9.5 years ago by ▴ 230 • written 9.6 years ago by ▴ 160
1
vote
5
replies
1.9k
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Help inputing sailfish TPM files into tximport
tximport sailfish
9.6 years ago • updated 9.5 years ago sjmonkley ▴ 40
7
votes
11
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7.1k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 9.5 years ago by ▴ 20 • written 9.9 years ago by ▴ 20
1
vote
2
replies
2.5k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 9.5 years ago by ★ 1.2k • written 11.2 years ago by ▴ 100
0
votes
8
replies
2.7k
views
significance of ChIPseq peak overlap
chipseeker
updated 9.5 years ago by ★ 1.2k • written 9.5 years ago by ▴ 10
3
votes
10
replies
8.6k
views
Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space in paired edgeR comparison
edger paired samples model.matrix estimatedisp
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 30
3
votes
4
replies
2.3k
views
Competitive gene set testing between two sets of genes
gene set testing camera edger
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 20
1
vote
7
replies
3.7k
views
dmpFinder return value (minfi)
minfi dmpfinder dmp illuminahumanmethylationepicanno.ilmn10b.hg19 epic microarray
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 120
0
votes
10
replies
3.4k
views
Getting rawdata for TMM normalization
normalization
9.6 years ago • updated 9.5 years ago humberto_munoz • 0
2
votes
5
replies
2.3k
views
makeOrgPackageFromNCBI for non model species -> eror in file
makeorgpackagefromncbi
updated 4.6 years ago by 6.7k • written 9.5 years ago by ▴ 20
0
votes
1
reply
2.1k
views
Efficient coverage calculation with RleList and GRanges
granges Rle coverage View mean
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 170
9
votes
16
replies
9.1k
views
edger, trended or common dispersion
edger
updated 9.5 years ago by ▴ 20 • written 10.1 years ago by ▴ 80
0
votes
1
reply
1.8k
views
bioconductor/release_core:20160630 - BiocInstaller version 3.2 is too old for R version 3.3.1
docker bioconductor
9.5 years ago Karl Forner ▴ 70
2
votes
1
reply
2.0k
views
polyester: adding noise to RNASeq counts?
rnaseq polyester
updated 9.5 years ago by ▴ 210 • written 9.6 years ago by • 0
9
votes
12
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
written 9.7 years ago by ▴ 20
46,726 results • Page 386 of 935
Recent ...
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by ATpoint ★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening in a clean install
Votes
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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