3
votes
18
replies
3.0k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 4 weeks ago shepherl 3.9k
2
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7
replies
3.0k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
7
votes
18
replies
3.0k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 4 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
1
vote
7
replies
3.0k
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Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
3
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4
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3.0k
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Protein differential Expression analysis
differential expression proteomics
updated 9 months ago by ★ 4.1k • written 6.4 years ago by • 0
0
votes
11
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2.9k
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edgeR contrasts
edgeR
updated 9 months ago by 66k • written 20 months ago by • 0
1
vote
2
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2.9k
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TPM to raw counts
salmon DESeq2
updated 5 months ago by • 0 • written 2.4 years ago by • 0
0
votes
5
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2.9k
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DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.2 years ago • updated 16 days ago Henrik Bengtsson ★ 2.4k
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 10 months ago by 42k • written 2.6 years ago by • 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 19 days ago by 66k • written 2.4 years ago by • 0
3
votes
10
replies
2.8k
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error in package GenVisR while installing
GenVisR GenVis
updated 6 months ago by ▴ 30 • written 22 months ago by • 0
1
vote
12
replies
2.8k
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How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 7 months ago by ★ 1.5k • written 22 months ago by • 0
0
votes
3
replies
2.8k
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Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 10 months ago by • 0 • written 19 months ago by • 0
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
7
votes
4
replies
2.8k
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Normalized counts of DESeq2 affected by design formula?
deseq2
updated 4 months ago by • 0 • written 6.2 years ago by ▴ 20
3
votes
6
replies
2.8k
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DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 12 weeks ago by • 0 • written 5.3 years ago by ▴ 50
6
votes
6
replies
2.8k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.1 years ago by ▴ 60
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by 50k • written 12.0 years ago by ▴ 180
1
vote
6
replies
2.7k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.5 years ago by ▴ 10
1
vote
4
replies
2.7k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
0
votes
2
replies
2.7k
views
How to get the rsID of 4 million SNPA
ensembldb SNP SNPData genomes
written 2.2 years ago by • 0
0
votes
4
replies
2.7k
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Error using Bsmooth.tstat due to NAs
Coverage bsseq
updated 6 months ago by • 0 • written 9.7 years ago by ★ 13k
2
votes
2
replies
2.6k
views
After having the output from SingleR for cell type annotation, what's the next step to assign the cell type to each cluster
SingleCellSignalR SingleCellWorkflow SingleR
updated 6 months ago by ★ 1.5k • written 3.0 years ago by ▴ 10
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 10
2
votes
6
replies
2.6k
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Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error cn.mops
updated 10 weeks ago by • 0 • written 6.4 years ago by ▴ 10
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 21 days ago by • 0 • written 4.6 years ago by ▴ 10
3
votes
11
replies
2.6k
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Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
12 months ago • updated 11 months ago Anna ▴ 20
0
votes
18
replies
2.6k
views
problem installing ENmix package
ENmix Bioconductor rtracklayer
written 3.2 years ago by • 0
0
votes
1
reply
2.6k
views
Warning messages in detecting P-values
minfiDataEPIC methylationArrayAnalysis
updated 9 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
2
replies
2.6k
views
vmatchPattern on DNAstring set
Bioconductor
9 months ago Avner • 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 9 months ago by • 0 • written 6.5 years ago by ▴ 10
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
0
votes
3
replies
2.5k
views
How to handle BSsmooth.tstat for single replicate samples? Error: need at least two non-NA values to interpolate
bsseq Bsmooth
updated 6 months ago by • 0 • written 9.2 years ago by • 0
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.5 years ago by ★ 13k
1
vote
12
replies
2.5k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 3 months ago by • 0 • written 2.6 years ago by ▴ 380
2
votes
7
replies
2.5k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 7 months ago by • 0 • written 3.4 years ago by ▴ 20
2
votes
2
replies
2.5k
views
Biostatistician Position: UMass Medical School
Microarray Microarray
written 16.9 years ago by ▴ 190
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib rhdf5
3.3 years ago • updated 9 months ago Thomas Sandmann ▴ 90
0
votes
3
replies
2.4k
views
internal error in trio library when trying to use lfmm() in LEA package
lfmm LEA
updated 8 weeks ago by • 0 • written 3.0 years ago by • 0
1
vote
1
reply
2.4k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 10 months ago by ★ 5.2k • written 10 months ago by ▴ 20
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago Luis • 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
2
votes
2
replies
2.3k
views
ComplexHeatmap: Change font size of annotation axis values
ComplexHeatmap
updated 9 months ago by • 0 • written 23 months ago by ▴ 10
0
votes
5
replies
2.3k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 10 months ago by ▴ 380 • written 7.0 years ago by • 0
0
votes
10
replies
2.3k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 5.1 years ago by • 0
3
votes
1
reply
2.3k
views
Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
written 3.6 years ago by ★ 2.0k
2
votes
3
replies
2.2k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 9 weeks ago by ★ 4.1k • written 2.1 years ago by ▴ 20
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 5 weeks ago by • 0 • written 8.0 years ago by ▴ 180
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 12 months ago by 50k • written 17 months ago by ▴ 20
0
votes
2
replies
2.2k
views
clusterProfiler - custom annotations
clusterProfiler
updated 4 months ago by ★ 4.0k • written 17 months ago by • 0
1,000 results • Page 3 of 20
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Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by mohammedtoufiq91 ▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
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