0
votes
7
replies
370
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 28 days ago hortense96 • 0
1
vote
7
replies
364
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
26 days ago • updated 25 days ago pl23 • 0
1
vote
4
replies
363
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
28 days ago • updated 26 days ago winwater0928 • 0
4
votes
5
replies
346
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
16 days ago • updated 6 days ago Chris ▴ 10
1
vote
0
replies
345
views
News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
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8 weeks ago • updated 7 days ago shepherl 3.9k
3
votes
1
reply
330
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 28 days ago by 42k • written 28 days ago by ▴ 40
0
votes
5
replies
328
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 27 days ago by 66k • written 4 weeks ago by • 0
5
votes
3
replies
323
views
Log-cpm values from limma
limma edgeR RNASeq
updated 12 days ago by 50k • written 4 weeks ago by • 0
2
votes
5
replies
320
views
get BM error
ensembldb
updated 27 days ago by 66k • written 28 days ago by • 0
1
vote
3
replies
313
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 14 days ago by ★ 4.1k • written 20 days ago by • 0
3
votes
5
replies
310
views
Help with running egsea()
EGSEA
15 days ago • updated 14 days ago Chris ▴ 10
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 days ago by ★ 1.4k • written 19 days ago by ▴ 130
0
votes
3
replies
308
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
1
vote
2
replies
301
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
21 days ago • updated 20 days ago Yveto • 0
4
votes
9
replies
299
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
3
votes
4
replies
299
views
Store output of matchPWM()
biostrings Biostrings
20 days ago • updated 8 days ago mat149 ▴ 70
2
votes
4
replies
297
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 29 days ago by 66k • written 4 weeks ago by • 0
2
votes
2
replies
292
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
14 days ago • updated 8 days ago zzrammal • 0
1
vote
2
replies
291
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
13 days ago • updated 12 days ago Dylan.Sheerin • 0
2
votes
3
replies
288
views
package goseq seems to be not available on the latest version of R
goseq
updated 15 days ago by 50k • written 18 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 21 days ago by 66k • written 22 days ago by • 0
3
votes
3
replies
276
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 22 days ago by ★ 4.1k • written 23 days ago by ▴ 10
3
votes
4
replies
274
views
Help with error using camera() in limma
CAMERA limma
21 days ago Chris ▴ 10
0
votes
5
replies
273
views
ChAMP installation issue
Cha ChAMP
updated 16 hours ago by 3.9k • written 9 days ago by • 0
0
votes
2
replies
270
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
29 days ago • updated 27 days ago shuwangxinze1996 • 0
0
votes
1
reply
268
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 21 days ago by 66k • written 22 days ago by • 0
0
votes
4
replies
267
views
Minfi - estimatecellscount
min minfi
updated 22 days ago by 66k • written 7 weeks ago by • 0
1
vote
3
replies
267
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 days ago by 50k • written 8 days ago by • 0
1
vote
2
replies
265
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
8 days ago • updated 5 days ago BioinfGuru ▴ 30
2
votes
3
replies
265
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 18 days ago by • 0
2
votes
5
replies
264
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 26 days ago by 66k • written 28 days ago by • 0
1
vote
3
replies
259
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 25 days ago by 42k • written 26 days ago by • 0
3
votes
3
replies
256
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
2
votes
5
replies
248
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
6 days ago • updated 4 days ago Patadù ▴ 10
0
votes
2
replies
246
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 weeks ago • updated 29 days ago catv • 0
3
votes
2
replies
242
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 29 days ago by ★ 4.0k • written 4 weeks ago by ▴ 10
1
vote
3
replies
242
views
Different Shrunk Log2FC according with reference
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 20
2
votes
2
replies
242
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
22 days ago Chris ▴ 10
2
votes
2
replies
240
views
fgsea significant result
fgsea
17 days ago • updated 16 days ago Chris ▴ 10
0
votes
3
replies
238
views
Couldn't connect to server while using "pathways"
graphite
updated 15 days ago by 42k • written 16 days ago by • 0
1
vote
4
replies
235
views
minfi::read.metharray.exp
minfiData minfi
updated 28 days ago by ▴ 780 • written 29 days ago by • 0
0
votes
3
replies
231
views
Differences in differential analysis methods for RNA-Seq
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updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
0
votes
2
replies
230
views
PCA plot suggestions
DESeq2 PCAtools
updated 25 days ago by 42k • written 27 days ago by • 0
0
votes
2
replies
228
views
Visium RNA
metaMSdata
written 9 weeks ago by • 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago kcarey • 0
1
vote
2
replies
219
views
Improving the design matrices vignette in RNAseq123
RNAseq123
29 days ago • updated 15 days ago Lluís Revilla Sancho ▴ 730
1
vote
2
replies
213
views
Citation for edgeR user guide
edgeR
written 28 days ago by ▴ 30
2
votes
4
replies
198
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 4 days ago by • 0
1
vote
1
reply
197
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 18 days ago by ▴ 10
2
votes
1
reply
194
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minfi latest update for EPIC V2 chip
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updated 14 days ago by 66k • written 15 days ago by • 0
180 results • Page 2 of 4
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Comment: slingshot: error with plot3d.SlingshotDataSet by Happiness • 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by mohammedtoufiq91 ▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
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