1
vote
15
replies
3.1k
views
Edge R Issue from a basic differential expression analysis
edger
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
0
votes
1
reply
2.1k
views
rGADEM error retrieving sequences
rgadem
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
0
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1
reply
2.0k
views
"Error in NSBS - subscript contains NAs or out-of-bounds indices" for bumphunter `matchGenes`
bumphunter
8.8 years ago jon.barenboim • 0
0
votes
1
reply
1.1k
views
Unable to define a CrisprSet because of missing target location
crisprvariants readstotarget
updated 8.8 years ago by • 0 • written 8.8 years ago by • 0
0
votes
4
replies
2.2k
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minfi "mapToGenome" dimension error
methylation epic microarray minfi methylationepic
8.8 years ago nhejazi • 0
0
votes
0
replies
1.4k
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[Gviz Error] Issue with plotTracks plotting ideogram track
gviz plottracks ideogramtrack
8.8 years ago cristianrohr768 • 0
0
votes
4
replies
2.4k
views
Installation of Bioconductor package: lpsymphony
lpsymphony
updated 8.8 years ago by ▴ 20 • written 8.8 years ago by ▴ 110
1
vote
6
replies
2.3k
views
Remove a list of specific probes from an HTAFeatureSet
pd.clariom.d.human affy probe
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 40
1
vote
8
replies
2.9k
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methylPipe meth.call issue with sorted SAM file
methylpipe
updated 4.7 years ago by • 0 • written 9.5 years ago by ▴ 10
0
votes
4
replies
1.8k
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TimmR error for hgu133a.db
software error annotate hgu133a
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
1
vote
4
replies
2.8k
views
Gviz sashimi read count
Gviz sashimi sashimi plots read counting bam
updated 8.8 years ago by ▴ 750 • written 8.8 years ago by • 0
0
votes
3
replies
1.7k
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Increased number of total exons in DEXSeq
dexseq exons grch37
8.8 years ago aditi ▴ 20
0
votes
4
replies
2.0k
views
BS genome non-model organism
bsgenome
8.9 years ago • updated 8.8 years ago minie • 0
0
votes
5
replies
8.9k
views
DESeq2 - I can't get the library to load
DESeq2
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
0
votes
6
replies
3.6k
views
not able to install geoquery package
microarrays xml RCurl libxml2 libcurl
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
2
votes
2
replies
2.8k
views
How to control p-value inflation with limma
limma pvalue inflation bacon
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 10
1
vote
7
replies
4.0k
views
Linear regression model in RNA seq
deseq2 limma R rnaseq
8.8 years ago Karl Fees ▴ 10
0
votes
0
replies
1.3k
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How to pathway analysis of Arabidopsis thaliana organism
microarray pathview
8.8 years ago avinash gupta ▴ 130
0
votes
0
replies
520
views
Does projectcelltype add to 1?
minfi
8.8 years ago jc114 • 0
0
votes
0
replies
1.5k
views
RPKM counts with SVA package & Combat with SVA?
batch effect combat sva sva
8.8 years ago Ahdee ▴ 60
0
votes
0
replies
1.3k
views
VariantAnnotation mapToTranscripts: best implementation
VariantAnnotation mapToTranscripts
8.8 years ago kristina_holton • 0
1
vote
0
replies
1.4k
views
Job: Bioinformatician/Computational Biologist opportunity at the University of Massachusetts Medical School
bioinformatician job Job
8.8 years ago Julie Zhu ★ 4.3k
2
votes
8
replies
6.8k
views
StringTie + Ballgown: handling biological replicates
ballgown stringtie
updated 8.8 years ago by • 0 • written 9.8 years ago by ▴ 10
0
votes
1
reply
925
views
How to extract .CEL files from .DTTfile/archive
microarray .CEL fiels .DTT tools
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
1
vote
6
replies
4.4k
views
Multiple testing limma contrasts
limma limma voom limma contrast matrix multiple testing correction
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 10
0
votes
5
replies
2.0k
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CRISPRseek prediction of truncated Nme sgRNA and getting error message
crisprseek
updated 8.8 years ago by ★ 4.3k • written 8.8 years ago by • 0
0
votes
0
replies
1.1k
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Visualizing motif instances in peak data
motifs TF peakset plots
8.8 years ago rbronste ▴ 60
2
votes
4
replies
2.8k
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TCGA - Different Sample Number
recount
updated 8.8 years ago by ▴ 20 • written 8.8 years ago by • 0
0
votes
3
replies
1.6k
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Get back to individual measures to calculate coefficients like the lmFit fucntion (limma package)
limma lmfit weight individual
8.8 years ago stephane.cauchi ▴ 10
2
votes
2
replies
1.5k
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pcaGoPromoter PCA plot in R: issue with EntrezID conversion
pca pca plot pcagopromoter
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 10
7
votes
3
replies
4.3k
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plotting correlation between samples
correlation
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 10
1
vote
5
replies
2.8k
views
Removing batch effect from microarray data
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updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 40
10
votes
4
replies
3.9k
views
Adjust for multiple batches using combat
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updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
0
votes
4
replies
5.3k
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error in sort.int , 'x' must be atomic in affy::boxplot
affy package boxplot hgu133plus2 oligo package
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 840
2
votes
2
replies
2.0k
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DESeq2 in phyloseq
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8.8 years ago sarahmacdonald86 • 0
8
votes
1
reply
11k
views
extracting the genes associated with the clusters
heatmap.2 pheatmap complexheatmap heatplus
updated 8.8 years ago by ▴ 690 • written 8.8 years ago by ▴ 670
0
votes
1
reply
1.7k
views
missMethyl package: gsameth bias plots
missmethyl plots bias package
updated 8.8 years ago by ▴ 40 • written 8.8 years ago by • 0
2
votes
3
replies
1.7k
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Issues about experiment design
limma model.matrix makecontrasts
8.8 years ago TFony ▴ 10
3
votes
5
replies
3.3k
views
txImport: a gene seems missing from the sample data
txImportData txImport
updated 4.9 years ago by 68k • written 8.8 years ago by • 0
0
votes
0
replies
1.1k
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Find drugs influencing specific genes
drug development
8.8 years ago bioinformatics ▴ 30
6
votes
7
replies
5.7k
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Dealing with (blood) contamination in RNA-seq data
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updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 90
5
votes
7
replies
2.6k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 40
0
votes
0
replies
1.2k
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HowTo: install just html help on top of existing packages
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8.8 years ago Malcolm Cook ★ 1.6k
1
vote
5
replies
3.3k
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how to plot human genome chromosome Ideogram with each length by Gviz
Gviz chromosome ideogram
updated 8.8 years ago by ▴ 150 • written 8.8 years ago by ▴ 10
0
votes
0
replies
1.7k
views
bumphunter P values and significance testing
minfi bumphunter
8.8 years ago cardenasca ▴ 40
2
votes
1
reply
1.6k
views
DESeq2 for read count input from 2 different NGS platforms
rnaseq deseq2
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by ▴ 60
1
vote
4
replies
8.0k
views
ClusterProfiler - How to : input file, groupGo, enrichGo
clusterprofiler input files error help
updated 8.8 years ago by ★ 1.2k • written 8.8 years ago by • 0
9
votes
8
replies
5.5k
views
heatmap of genes based on enriched GO categories
goexpress gopro
8.8 years ago Bogdan ▴ 670
17
votes
5
replies
4.9k
views
Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
IRanges
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 20
0
votes
5
replies
1.9k
views
goseq - supportedOrganisms error
go goseq
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
46,696 results • Page 344 of 934
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Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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