0
votes
7
replies
758
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
11 weeks ago • updated 27 days ago shepherl 3.9k
7
votes
6
replies
639
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 15 days ago by • 0
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
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updated 3 days ago by • 0 • written 5.5 years ago by ★ 4.0k
0
votes
44
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3.2k
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 6 days ago by 42k • written 15 months ago by • 0
10
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10
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1.9k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 5 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
0
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5
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2.9k
views
DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.2 years ago • updated 15 days ago Henrik Bengtsson ★ 2.4k
0
votes
4
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1.2k
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News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 3 days ago by • 0 • written 19 months ago by ▴ 70
6
votes
19
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2.6k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 20 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
6
replies
306
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 days ago by ★ 1.4k • written 18 days ago by ▴ 130
0
votes
2
replies
145
views
Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 6 days ago by ▴ 10 • written 8 days ago by • 0
3
votes
4
replies
293
views
Store output of matchPWM()
biostrings Biostrings
19 days ago • updated 7 days ago mat149 ▴ 70
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 20 days ago by • 0 • written 13.1 years ago by ▴ 10
4
votes
5
replies
343
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
15 days ago • updated 5 days ago Chris ▴ 10
6
votes
12
replies
5.1k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 28 days ago shepherl 3.9k
0
votes
3
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9.4k
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SingleR Label.Ont
SingleR
updated 9 days ago by • 0 • written 8 months ago by • 0
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago Chris ▴ 10
4
votes
9
replies
496
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Memory errors using read.bismark?
dmrseq bsseq
5 weeks ago • updated 13 days ago Juan Higareda • 0
1
vote
2
replies
95
views
Subsetting RNAseq data | voomaByGroup()
limma
2 days ago • updated 17 hours ago Anna • 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro clustering
updated 3 days ago by • 0 • written 7.9 years ago by • 0
2
votes
4
replies
292
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 28 days ago by 66k • written 4 weeks ago by • 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 17 days ago by 50k • written 17 days ago by • 0
0
votes
2
replies
172
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
21 days ago • updated 17 days ago Aurora • 0
0
votes
1
reply
163
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 18 days ago by 50k • written 18 days ago by • 0
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
25 days ago • updated 24 days ago pl23 • 0
1
vote
2
replies
113
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Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
6 days ago • updated 5 days ago Patadù ▴ 10
0
votes
1
reply
186
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
1
vote
5
replies
1.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 13 days ago by • 0 • written 5 months ago by • 0
0
votes
2
replies
217
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
0
votes
3
replies
134
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 5 days ago by 42k • written 6 days ago by • 0
3
votes
1
reply
329
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 40
3
votes
10
replies
493
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 10 days ago by 66k • written 13 days ago by • 0
0
votes
8
replies
524
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 6 days ago by ▴ 30 • written 7 days ago by • 0
0
votes
1
reply
167
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 26 days ago by 42k • written 26 days ago by • 0
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 7 days ago by • 0 • written 3.6 years ago by ▴ 60
1
vote
1
reply
51
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 16 hours ago by 66k • written 23 hours ago by • 0
1
vote
2
replies
755
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 24 days ago Patadù ▴ 10
1
vote
1
reply
79
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 16 hours ago by 66k • written 1 day ago by • 0
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 21 days ago by ★ 4.1k • written 22 days ago by ▴ 10
1
vote
2
replies
177
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
26 days ago • updated 25 days ago ATpoint ★ 4.1k
0
votes
5
replies
143
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC batchinDeseq2. columnsincolData.
1 day ago • updated 18 hours ago Galina • 0
0
votes
1
reply
115
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
4
replies
148
views
error running enricher from clusterprofiler
clusterProfiler cluster
5 days ago Yael • 0
5
votes
3
replies
320
views
Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 4 weeks ago by • 0
1
vote
3
replies
238
views
Different Shrunk Log2FC according with reference
DESeq2
updated 26 days ago by 42k • written 26 days ago by ▴ 20
0
votes
3
replies
283
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 20 days ago by 66k • written 21 days ago by • 0
1
vote
2
replies
138
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
6 days ago • updated 5 days ago Daniel • 0
0
votes
5
replies
325
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 26 days ago by 66k • written 29 days ago by • 0
0
votes
1
reply
139
views
FDR via q-value
qvalue
updated 28 days ago by 66k • written 4 weeks ago by • 0
2
votes
2
replies
240
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago Chris ▴ 10
170 results • Page 1 of 4
Recent ...
Replies
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
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