0
votes
1
reply
375
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 10 months ago by 68k • written 10 months ago by • 0
0
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2
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1.3k
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
10 months ago Blandine • 0
0
votes
5
replies
725
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 months ago by • 0
0
votes
1
reply
454
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affymetrix
genomes Annotation
updated 10 months ago by 68k • written 10 months ago by • 0
0
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1
reply
2.0k
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Problems with GSEA
GSEABase
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
1
reply
498
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Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
10 months ago ja.garcia • 0
0
votes
4
replies
964
views
How to sort negative log2FC or FC in RNAseq for GSEA?
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10 months ago Quang NN ▴ 10
2
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4
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915
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EdgeR Biological CVs
edgeR
written 10 months ago by • 0
0
votes
1
reply
498
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
249
views
Problem with PCAtool as dependencie
COTAN PCAtools
10 months ago Silvia • 0
1
vote
2
replies
457
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Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 12 months ago by • 0
0
votes
0
replies
293
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cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
10 months ago xiaofeiwang18266 ▴ 60
3
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5
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2.1k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 10 months ago by 68k • written 10 months ago by ▴ 10
0
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1
reply
402
views
XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
2
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1.6k
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Error using useMart or useEnsembl
biomaRt
updated 10 months ago by 68k • written 10 months ago by • 0
2
votes
1
reply
758
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Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 10 months ago by 68k • written 10 months ago by ▴ 60
0
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11
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1.4k
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
2
replies
949
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DESeq2 Heatmap
heatmaps
updated 10 months ago by ★ 1.4k • written 10 months ago by • 0
0
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4
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1.8k
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Biomart and ensembl not working?
ensembldb biomaRt
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
308
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Unknown gene transcripts after annotatr
annotatr
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
329
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Improve performance of qusage aggregateGeneSet
qusage
updated 10 months ago by 68k • written 10 months ago by • 0
0
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0
replies
321
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gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
10 months ago nurkenber • 0
0
votes
0
replies
382
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
10 months ago GJ • 0
0
votes
1
reply
393
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 10 months ago by 68k • written 10 months ago by ▴ 20
0
votes
0
replies
501
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News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
10 months ago info ▴ 10
0
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2
replies
673
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Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 11 months ago by ▴ 840
0
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2
replies
850
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iam not able to do retrive data using GEOquery R package
HELP
updated 11 months ago by 68k • written 11 months ago by • 0
2
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5
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803
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Differential variability modelling with vst() expression
limma DESeq2
written 11 months ago by • 0
0
votes
2
replies
487
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Installation error for Rsamtools.
Rsamtools
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
3
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9
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2.0k
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Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi EnsDb.Mmusculus.v79 biomaRt org.Mm.eg.db
updated 10 months ago by • 0 • written 11 months ago by • 0
0
votes
3
replies
916
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 11 months ago by • 0
0
votes
2
replies
912
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 8 months ago by • 0 • written 11 months ago by • 0
2
votes
9
replies
1.7k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
11 months ago • updated 10 months ago Quang NN ▴ 10
0
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5
replies
837
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Diffbind interpretation of data - fold change
DiffBind
11 months ago Vera • 0
1
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1
reply
894
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
1
reply
578
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No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 11 months ago by 68k • written 11 months ago by • 0
1
vote
2
replies
3.3k
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Package `not available for Bioconductor version '3.20'` when it should be
consensusOV genefu
11 months ago Levi Waldron ★ 1.1k
0
votes
0
replies
349
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Trouble with double delimiters in .fcs file (flowCore package)
flowCore FlowCytometry FlowCytometryData
11 months ago vpochic • 0
0
votes
4
replies
571
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Newbie Question - adding metadata to an analysis
Biobase
11 months ago Bryan H • 0
0
votes
1
reply
339
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by • 0
0
votes
2
replies
646
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MissMethyl failed to use gometh function for EPICv2
missMethyl EPICv2manifest
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
465
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Correlation between gene clusters
genomes RNASeqData
written 11 months ago by • 0
0
votes
2
replies
714
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Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
11 months ago gingergeiger22 • 0
0
votes
1
reply
603
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
2
votes
1
reply
728
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
1
reply
1.7k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 11 months ago by • 0 • written 4.0 years ago by ▴ 60
6
votes
5
replies
1.1k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 11 months ago by 68k • written 11 months ago by • 0
1
vote
8
replies
1.6k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
11 months ago Andre • 0
0
votes
2
replies
713
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
11 months ago Kucsera • 0
0
votes
1
reply
613
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 11 months ago by • 0 • written 11 months ago by • 0
46,691 results • Page 10 of 934
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Replies
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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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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