15
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23
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2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
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5 weeks ago • updated 9 days ago Chris • 0
14
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17
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Why p value inconsistent when using different number of pathway score?
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19 days ago • updated 8 days ago Chris • 0
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Theoretical WGCNA Question
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updated 21 days ago by • 0 • written 9.1 years ago by ▴ 150
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12
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Multi factor design edgeR/Deseq2
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updated 21 days ago by • 0 • written 8.8 years ago by ▴ 30
8
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7
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 days ago by • 0 • written 6.7 years ago by ▴ 80
8
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23
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972
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Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 28 days ago by ★ 3.3k • written 29 days ago by ▴ 40
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12
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
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6 months ago • updated 17 days ago shepherl 3.9k
6
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5
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Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC minifi
written 10 weeks ago by • 0
6
votes
19
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2.5k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 9 days ago by • 0 • written 4.6 years ago by ▴ 10
6
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10
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1.7k
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Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 20 days ago by • 0 • written 15 months ago by ▴ 10
6
votes
10
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2.2k
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overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 25 days ago by • 0 • written 8.0 years ago by ▴ 180
5
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6
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436
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 26 days ago by ★ 4.1k • written 4 weeks ago by ▴ 30
5
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9
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Batch correction and repeated measures
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updated 22 days ago by 50k • written 7 months ago by ▴ 10
5
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8
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Limma design with continuous and categorical covariates
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updated 16 days ago by • 0 • written 7.7 years ago by ▴ 30
5
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9
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936
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Light difference when using coef vs omit a group when compare 3 groups.
limma
29 days ago • updated 21 days ago Chris • 0
5
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6
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2.8k
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 7 days ago by 65k • written 2.3 years ago by • 0
4
votes
9
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436
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Memory errors using read.bismark?
dmrseq bsseq
28 days ago • updated 2 days ago Juan Higareda • 0
4
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0
replies
98
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
8 days ago shepherl 3.9k
4
votes
6
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443
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FilterByExpr low counts with small sample size
edgeR
22 days ago • updated 17 days ago Jonathan ▴ 10
4
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2
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568
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
7 days ago • updated 3 days ago gene_bioconductor ▴ 10
3
votes
3
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350
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permutation test in edgeR
rna-seq edgeR
updated 18 days ago by 50k • written 4 weeks ago by • 0
3
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4
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219
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 2 days ago by 50k • written 4 days ago by • 0
3
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3
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218
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Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
27 days ago • updated 21 days ago jacques.imbert • 0
3
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5
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204
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Help with running egsea()
EGSEA
3 days ago • updated 1 day ago Chris • 0
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18
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News: List of Deprecated Packages for Bioc3.18
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10 months ago • updated 22 days ago shepherl 3.9k
3
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4
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437
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 1 day ago by ★ 6.5k • written 4 days ago by • 0
3
votes
1
reply
756
views
News: [Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv spatialLIBD News
written 4.2 years ago by ★ 1.0k
3
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1
reply
316
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 15 days ago by 42k • written 16 days ago by ▴ 40
3
votes
4
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233
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Help with error using camera() in limma
CAMERA limma
9 days ago Chris • 0
3
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1
reply
1.5k
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Job: Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job Job machine learning deep learning computational biology
written 6.3 years ago by ▴ 180
3
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3
replies
234
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Log-cpm values from limma
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updated 1 hour ago by 50k • written 21 days ago by • 0
3
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1
reply
101
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How to save the DEXSeq results
DEXSeq
updated 3 days ago by 42k • written 3 days ago by • 0
3
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1
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1.5k
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Limma without eBayes, is it indistunguishable from Ordinary Least Square?
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updated 1 day ago by 50k • written 5.6 years ago by ▴ 10
3
votes
6
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283
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Surrogate variable analysis for paired RNA seq experiment
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28 days ago nhaus ▴ 30
3
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3
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244
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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updated 10 days ago by ★ 4.1k • written 10 days ago by ▴ 10
3
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3
replies
233
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
3
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2
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220
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Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 17 days ago by ★ 3.9k • written 20 days ago by ▴ 10
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 22 days ago by • 0 • written 11 months ago by • 0
2
votes
3
replies
194
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package goseq seems to be not available on the latest version of R
goseq
updated 3 days ago by 50k • written 6 days ago by ▴ 20
2
votes
2
replies
176
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fgsea significant result
fgsea
5 days ago • updated 4 days ago Chris • 0
2
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2
replies
195
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OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 20 days ago by 65k • written 21 days ago by • 0
2
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5
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278
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get BM error
ensembldb
updated 15 days ago by 65k • written 15 days ago by • 0
2
votes
2
replies
202
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
27 days ago julia_mcdonough • 0
2
votes
3
replies
200
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 4 days ago by ★ 4.1k • written 6 days ago by • 0
2
votes
13
replies
439
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Trying to use enrichGO
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18 days ago • updated 15 days ago fernanda.backsouza ▴ 10
2
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2
replies
395
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
28 days ago • updated 27 days ago Henry ▴ 10
2
votes
9
replies
403
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 14 days ago by 65k • written 14 days ago by • 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 14 days ago by 65k • written 16 days ago by • 0
2
votes
2
replies
178
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ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
27 days ago • updated 24 days ago daniel.carbajo • 0
2
votes
2
replies
173
views
[DiffBind] Obtaining normalization factors
DiffBind
27 days ago • updated 23 days ago Henry ▴ 10
199 results • Page 1 of 4
Recent ...
Replies
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data by Abbey • 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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