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4
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2.2k
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News: EuroBioC2023 abstract submission closing soon!
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Cross-validation with multiple control subgroups in limma
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11 months ago Ali Barry ▴ 40
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553
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
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updated 11 months ago by 43k • written 12 months ago by • 0
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ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
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Error in get_anno_data(ontology) : ontology not supported yet...
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11 months ago GODseeker • 0
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Standardization of rlog transformed counts before PCA
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updated 11 months ago by ★ 5.0k • written 11 months ago by ▴ 10
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updated 11 months ago by • 0 • written 11 months ago by • 0
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Limma - using both array and spot weights in lmFit
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updated 11 months ago by ★ 1.1k • written 12 months ago by • 0
0
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298
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Errors running learn.bn function from Pigengene in windows environment
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written 11 months ago by • 0
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2
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Need new version : tx2gene.gencode.v47.csv
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11 months ago • updated 6 months ago Gaurav • 0
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Deseq2 Design
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updated 11 months ago by 68k • written 11 months ago by • 0
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p value is 0, padj is 0
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12 months ago • updated 11 months ago Wirayatida • 0
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Cannot install GO.db and org.Hs.eg.db
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updated 11 months ago by 68k • written 12 months ago by • 0
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Help using rtracklayer for gene ID extraction
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1
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2
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
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12 months ago georgii.vdovin • 0
0
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1
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877
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Feature Counts -R XS Read Assignment Tag
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updated 12 months ago by 53k • written 21 months ago by • 0
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prebs
12 months ago 2zrcj3448p 0
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Matching patterns in an AAStringset
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updated 12 months ago by ▴ 70 • written 12 months ago by • 0
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
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12 months ago Tadeoye ▴ 20
0
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7
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
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updated 12 months ago by • 0 • written 12 months ago by • 0
2
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4
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Can we get beta values with DMRcate package
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12 months ago Melisa Tecik • 0
2
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12 months ago SamGG ▴ 360
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RSubread output significantly different from bash Subread output
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updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
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12 months ago cailing20 • 0
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
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updated 12 months ago by 43k • written 12 months ago by ▴ 20
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12 months ago Jiping Wang ▴ 90
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How to annotate a limma Elist raw class object with an annotation file
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747
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DESeq2 - Comparing Comparisons
DESeq2
updated 12 months ago by 68k • written 12 months ago by • 0
0
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0
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288
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12 months ago Adelyn • 0
0
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4
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12 months ago anon • 0
0
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0
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429
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12 months ago Edward • 0
1
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4
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12 months ago Philippine • 0
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scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
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updated 12 months ago by ★ 29k • written 12 months ago by ▴ 10
1
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2
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contrast matrix design for a continuous variable
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12 months ago • updated 10 months ago dtzhu337 • 0
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DESeq2- merging technical vs biological replicates
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updated 12 months ago by 43k • written 12 months ago by • 0
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updated 12 months ago by 43k • written 12 months ago by • 0
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updated 12 months ago by • 0 • written 12 months ago by • 0
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how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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12 months ago • updated 9 months ago xiaofeiwang198266 • 0
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Crossover design with limma
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updated 11 months ago by 53k • written 12 months ago by ▴ 30
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updated 12 months ago by 68k • written 12 months ago by • 0
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updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
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497
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rrvgo::calculateSimMatrix() error
rrvgo
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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12 months ago Daphne • 0
0
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2
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DESeq2 sizefactors counfounded with biological treatment
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12 months ago Anna • 0
46,691 results • Page 11 of 934
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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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