0
votes
1
reply
120
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 10 days ago by 42k • written 11 days ago by • 0
0
votes
0
replies
82
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
10 days ago Maria Doyle ▴ 70
0
votes
1
reply
107
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 10 days ago by 3.9k • written 10 days ago by • 0
0
votes
1
reply
123
views
putting my own expression data in deseq2
DESeq2
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
2
votes
2
replies
214
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
11 days ago Chris • 0
0
votes
3
replies
256
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 10 days ago by 65k • written 11 days ago by • 0
0
votes
0
replies
84
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
11 days ago Chris • 0
3
votes
3
replies
249
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 11 days ago by ★ 4.1k • written 11 days ago by ▴ 10
1
vote
1
reply
138
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 14 days ago by ▴ 40 • written 14 days ago by ★ 1.5k
0
votes
2
replies
216
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PCA plot suggestions
DESeq2 PCAtools
updated 14 days ago by 42k • written 15 days ago by • 0
1
vote
3
replies
236
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 14 days ago by 42k • written 15 days ago by • 0
0
votes
1
reply
146
views
ATACseq merge peaks
DiffBind
updated 14 days ago by ★ 4.1k • written 16 days ago by • 0
1
vote
2
replies
196
views
Improving the design matrices vignette in RNAseq123
RNAseq123
18 days ago • updated 4 days ago Lluís Revilla Sancho ▴ 730
1
vote
7
replies
338
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
15 days ago • updated 14 days ago pl23 • 0
2
votes
9
replies
406
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 15 days ago by 65k • written 15 days ago by • 0
0
votes
0
replies
132
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
15 days ago • updated 7 days ago glaciya2018 • 0
1
vote
2
replies
167
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
16 days ago • updated 15 days ago ATpoint ★ 4.1k
0
votes
1
reply
159
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 16 days ago by 42k • written 16 days ago by • 0
0
votes
0
replies
94
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
16 days ago • updated 11 days ago Sara • 0
2
votes
5
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283
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get BM error
ensembldb
updated 16 days ago by 65k • written 16 days ago by • 0
2
votes
5
replies
250
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 15 days ago by 65k • written 17 days ago by • 0
0
votes
0
replies
91
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
16 days ago Dario Strbenac ★ 1.5k
1
vote
3
replies
224
views
Different Shrunk Log2FC according with reference
DESeq2
updated 16 days ago by 42k • written 16 days ago by ▴ 20
1
vote
4
replies
344
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
16 days ago • updated 14 days ago winwater0928 • 0
3
votes
1
reply
319
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 17 days ago by 42k • written 17 days ago by ▴ 40
1
vote
1
reply
184
views
Citation for edgeR user guide
edgeR
updated 17 days ago by 50k • written 17 days ago by ▴ 30
0
votes
7
replies
724
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
10 weeks ago • updated 17 days ago shepherl 3.9k
1
vote
1
reply
122
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Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 17 days ago by 65k • written 17 days ago by ▴ 10
0
votes
8
replies
362
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 15 days ago by ★ 1.4k • written 17 days ago by • 0
0
votes
0
replies
76
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News: Interested in the analysis of Spatial Omics data?
tidySpatialExperiment SpatialExperiment MoleculeExperiment
17 days ago info ▴ 10
1
vote
4
replies
213
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minfi::read.metharray.exp
minfiData minfi
updated 16 days ago by ▴ 780 • written 18 days ago by • 0
0
votes
2
replies
259
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
17 days ago • updated 15 days ago shuwangxinze1996 • 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 18 days ago by ▴ 180 • written 14 months ago by ▴ 10
0
votes
2
replies
174
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 18 days ago by • 0
3
votes
3
replies
235
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
1
vote
4
replies
253
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 18 days ago by 65k • written 22 days ago by • 0
0
votes
1
reply
131
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FDR via q-value
qvalue
updated 18 days ago by 65k • written 21 days ago by • 0
0
votes
5
replies
307
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Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 16 days ago by 65k • written 19 days ago by • 0
0
votes
2
replies
223
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
21 days ago • updated 18 days ago catv • 0
0
votes
3
replies
1.2k
views
News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 19 days ago by • 0 • written 18 months ago by ▴ 70
6
votes
12
replies
5.0k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 18 days ago shepherl 3.9k
2
votes
13
replies
449
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
19 days ago • updated 16 days ago fernanda.backsouza ▴ 10
0
votes
0
replies
86
views
Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
19 days ago vaxahey107 • 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
20 days ago • updated 9 days ago Chris • 0
0
votes
0
replies
102
views
I am trying to detect alternative splicing.
ASpli
20 days ago Sebashish • 0
3
votes
2
replies
220
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 18 days ago by ★ 3.9k • written 21 days ago by ▴ 10
0
votes
3
replies
164
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 21 days ago by 65k • written 21 days ago by ▴ 30
2
votes
2
replies
198
views
OrgDb for maize
clusterProfiler OrgDb biomaRt Zea_mays
updated 21 days ago by 65k • written 22 days ago by • 0
1
vote
0
replies
309
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
21 days ago BioinfGuru ▴ 30
4
votes
6
replies
446
views
FilterByExpr low counts with small sample size
edgeR
23 days ago • updated 18 days ago Jonathan ▴ 10
197 results • Page 2 of 4
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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