15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 7 days ago Chris • 0
14
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17
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1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
17 days ago • updated 6 days ago Chris • 0
11
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5
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Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 19 days ago by • 0 • written 9.1 years ago by ▴ 150
9
votes
12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 19 days ago by • 0 • written 8.8 years ago by ▴ 30
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by • 0 • written 6.7 years ago by ▴ 80
8
votes
23
replies
957
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 26 days ago by ★ 3.3k • written 27 days ago by ▴ 40
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 24 days ago by • 0 • written 8.0 years ago by ▴ 180
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 18 days ago by • 0 • written 15 months ago by ▴ 10
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 15 days ago shepherl 3.9k
6
votes
19
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2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 7 days ago by • 0 • written 4.6 years ago by ▴ 10
6
votes
5
replies
445
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC minifi
written 9 weeks ago by • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 14 days ago by • 0 • written 7.7 years ago by ▴ 30
5
votes
6
replies
433
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 24 days ago by ★ 4.1k • written 28 days ago by ▴ 30
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 5 days ago by 65k • written 2.3 years ago by • 0
5
votes
9
replies
932
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
27 days ago • updated 19 days ago Chris • 0
5
votes
9
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1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 20 days ago by 50k • written 7 months ago by ▴ 10
4
votes
6
replies
438
views
FilterByExpr low counts with small sample size
edgeR
20 days ago • updated 15 days ago Jonathan ▴ 10
4
votes
9
replies
435
views
Memory errors using read.bismark?
dmrseq bsseq
26 days ago • updated 14 hours ago Juan Higareda • 0
4
votes
2
replies
545
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
5 days ago • updated 1 day ago gene_bioconductor ▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 3 hours ago by 50k • written 5.6 years ago by ▴ 10
3
votes
4
replies
221
views
Help with error using camera() in limma
CAMERA limma
7 days ago Chris • 0
3
votes
4
replies
179
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 7 hours ago by 50k • written 2 days ago by • 0
3
votes
0
replies
85
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
6 days ago shepherl 3.9k
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 14 days ago by 42k • written 14 days ago by ▴ 40
3
votes
2
replies
217
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 15 days ago by ★ 3.9k • written 18 days ago by ▴ 10
3
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6
replies
280
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
26 days ago nhaus ▴ 30
3
votes
3
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214
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Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
25 days ago • updated 19 days ago jacques.imbert • 0
3
votes
5
replies
172
views
Help with running egsea()
EGSEA
1 day ago • updated 2 hours ago Chris • 0
3
votes
18
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2.9k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 20 days ago shepherl 3.9k
3
votes
3
replies
340
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permutation test in edgeR
rna-seq edgeR
updated 17 days ago by 50k • written 29 days ago by • 0
3
votes
1
reply
1.5k
views
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
votes
3
replies
231
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 days ago by 42k • written 15 days ago by • 0
3
votes
1
reply
81
views
How to save the DEXSeq results
DEXSeq
updated 1 day ago by 42k • written 1 day ago by • 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 19 days ago by • 0
3
votes
3
replies
241
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 8 days ago by ★ 4.1k • written 9 days ago by ▴ 10
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
2
votes
2
replies
193
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 18 days ago by 65k • written 19 days ago by • 0
2
votes
5
replies
276
views
get BM error
ensembldb
updated 13 days ago by 65k • written 13 days ago by • 0
2
votes
3
replies
170
views
package goseq seems to be not available on the latest version of R
goseq
updated 1 day ago by 50k • written 4 days ago by ▴ 20
2
votes
2
replies
198
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
25 days ago julia_mcdonough • 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 20 days ago by • 0 • written 10 months ago by • 0
2
votes
2
replies
392
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
26 days ago • updated 25 days ago Henry ▴ 10
2
votes
2
replies
144
views
fgsea significant result
fgsea
3 days ago • updated 2 days ago Chris • 0
2
votes
9
replies
394
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 days ago by 65k • written 12 days ago by • 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 7 days ago by • 0 • written 7.9 years ago by • 0
2
votes
2
replies
203
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
8 days ago Chris • 0
2
votes
3
replies
329
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
23 days ago • updated 22 days ago daniel.carbajo • 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
25 days ago • updated 21 days ago Henry ▴ 10
2
votes
3
replies
183
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 2 days ago by ★ 4.1k • written 4 days ago by • 0
2
votes
2
replies
175
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
25 days ago • updated 23 days ago daniel.carbajo • 0
203 results • Page 1 of 5
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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