1
vote
2
replies
394
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 12 days ago by 50k • written 12 days ago by • 0
2
votes
3
replies
258
views
package goseq seems to be not available on the latest version of R
goseq
updated 9 days ago by 50k • written 12 days ago by ▴ 20
2
votes
3
replies
247
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 days ago by ★ 4.1k • written 12 days ago by • 0
0
votes
0
replies
115
views
dba.plotProfile() plotting and interpretation
DiffBind
12 days ago Henry ▴ 10
0
votes
1
reply
169
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 13 days ago by 50k • written 13 days ago by • 0
0
votes
1
reply
152
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 13 days ago by 50k • written 13 days ago by • 0
4
votes
2
replies
617
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
13 days ago • updated 9 days ago gene_bioconductor ▴ 10
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
13 days ago tholmes • 0
0
votes
2
replies
156
views
DESeq2 v1.35.0
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
13 days ago yvonneh • 0
0
votes
0
replies
81
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
13 days ago Ian D. ▴ 70
0
votes
1
reply
126
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 13 days ago by • 0
0
votes
4
replies
354
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 4 days ago by • 0 • written 15 days ago by ▴ 70
0
votes
2
replies
204
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
14 days ago • updated 13 days ago kcarey • 0
0
votes
3
replies
205
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 days ago by ★ 4.1k • written 14 days ago by • 0
1
vote
3
replies
298
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 8 days ago by ★ 4.1k • written 14 days ago by • 0
4
votes
0
replies
129
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
14 days ago shepherl 3.9k
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
fgsea
14 days ago • updated 12 days ago Chris ▴ 10
0
votes
3
replies
298
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 14 days ago by 42k • written 15 days ago by • 0
1
vote
2
replies
281
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
15 days ago • updated 14 days ago Yveto • 0
0
votes
1
reply
260
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 15 days ago by 65k • written 16 days ago by • 0
3
votes
4
replies
257
views
Help with error using camera() in limma
CAMERA limma
15 days ago Chris ▴ 10
1
vote
1
reply
149
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
2
replies
162
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
16 days ago • updated 13 days ago Aurora • 0
0
votes
1
reply
135
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 15 days ago by 42k • written 16 days ago by • 0
0
votes
0
replies
92
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
15 days ago Maria Doyle ▴ 70
0
votes
1
reply
119
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 15 days ago by 3.9k • written 16 days ago by • 0
0
votes
1
reply
133
views
putting my own expression data in deseq2
DESeq2
updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
2
votes
2
replies
229
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
16 days ago Chris ▴ 10
0
votes
3
replies
270
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 15 days ago by 65k • written 16 days ago by • 0
0
votes
0
replies
91
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
16 days ago Chris ▴ 10
3
votes
3
replies
261
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 17 days ago by ★ 4.1k • written 17 days ago by ▴ 10
1
vote
1
reply
150
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 19 days ago by ▴ 40 • written 19 days ago by ★ 1.5k
0
votes
2
replies
225
views
PCA plot suggestions
DESeq2 PCAtools
updated 19 days ago by 42k • written 21 days ago by • 0
1
vote
3
replies
249
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 19 days ago by 42k • written 20 days ago by • 0
0
votes
1
reply
165
views
ATACseq merge peaks
DiffBind
updated 19 days ago by ★ 4.1k • written 21 days ago by • 0
1
vote
2
replies
211
views
Improving the design matrices vignette in RNAseq123
RNAseq123
24 days ago • updated 9 days ago Lluís Revilla Sancho ▴ 730
1
vote
7
replies
352
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
20 days ago • updated 19 days ago pl23 • 0
2
votes
9
replies
423
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 20 days ago by 65k • written 20 days ago by • 0
0
votes
0
replies
141
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
21 days ago • updated 13 days ago glaciya2018 • 0
1
vote
2
replies
173
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
21 days ago ATpoint ★ 4.1k
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 21 days ago by 42k • written 21 days ago by • 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
21 days ago • updated 17 days ago Sara • 0
2
votes
5
replies
300
views
get BM error
ensembldb
updated 21 days ago by 65k • written 22 days ago by • 0
2
votes
5
replies
257
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 20 days ago by 65k • written 22 days ago by • 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
21 days ago Dario Strbenac ★ 1.5k
1
vote
3
replies
234
views
Different Shrunk Log2FC according with reference
DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 20
1
vote
4
replies
353
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
22 days ago • updated 20 days ago winwater0928 • 0
3
votes
1
reply
327
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 22 days ago by 42k • written 22 days ago by ▴ 40
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 22 days ago by ▴ 30
1,000 results • Page 2 of 20
Recent ...
Replies
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by pangtaihin • 0
Thank you very much ATpoint, but DESeq2, edgeR, limma are not specialized time-course framework, I think we might seek for another framewor…
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by ATpoint ★ 4.1k
High counts are generally less prone to noise compared to low counts. Bottom line is that you should stick to specialized testing framework…
Comment: Problem installing ChAMP on a MacBook by ATpoint ★ 4.1k
Did you run these lines? https://www.bioconductor.org/packages/release/bioc/html/ChAMP.html It is good practice to include code and error …
Comment: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 220
Looks like `sgv_pred` does not have the expected format. Was it created or edited manually? I would always recommend creating objects with …
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by pangtaihin • 0
Thank you:)
Votes
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
Answer: Can DESeq2 rlog normalized matrix reflects time course result directly?
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Answer: Trim/Filter out-of-bounds GRanges
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