1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
25 days ago • updated 24 days ago pl23 • 0
4
votes
5
replies
343
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
15 days ago • updated 6 days ago Chris ▴ 10
1
vote
0
replies
341
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News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition Awards Bioconductor Bioc204
8 weeks ago • updated 6 days ago shepherl 3.9k
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
0
votes
5
replies
326
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 26 days ago by 66k • written 29 days ago by • 0
5
votes
3
replies
320
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Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 4 weeks ago by • 0
2
votes
5
replies
318
views
get BM error
ensembldb
updated 26 days ago by 66k • written 27 days ago by • 0
1
vote
3
replies
307
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by ★ 4.1k • written 19 days ago by • 0
0
votes
6
replies
307
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
3
votes
5
replies
307
views
Help with running egsea()
EGSEA
14 days ago • updated 13 days ago Chris ▴ 10
0
votes
3
replies
305
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
3
votes
4
replies
296
views
Store output of matchPWM()
biostrings Biostrings
19 days ago • updated 7 days ago mat149 ▴ 70
1
vote
2
replies
296
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
20 days ago • updated 19 days ago Yveto • 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
1
vote
2
replies
288
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
12 days ago • updated 11 days ago Dylan.Sheerin • 0
4
votes
9
replies
287
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
2
votes
2
replies
287
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
13 days ago • updated 8 days ago zzrammal • 0
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
2
votes
3
replies
281
views
package goseq seems to be not available on the latest version of R
goseq
updated 15 days ago by 50k • written 17 days ago by ▴ 20
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 22 days ago by ★ 4.1k • written 22 days ago by ▴ 10
3
votes
4
replies
270
views
Help with error using camera() in limma
CAMERA limma
20 days ago Chris ▴ 10
0
votes
2
replies
268
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
28 days ago • updated 26 days ago shuwangxinze1996 • 0
0
votes
4
replies
267
views
Minfi - estimatecellscount
min minfi
updated 22 days ago by 66k • written 7 weeks ago by • 0
0
votes
1
reply
267
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 20 days ago by 66k • written 21 days ago by • 0
2
votes
3
replies
264
views
Too many significant genes when integrating gtex and tcga
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updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
2
votes
5
replies
263
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 25 days ago by 66k • written 27 days ago by • 0
1
vote
3
replies
263
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 days ago by 50k • written 7 days ago by • 0
1
vote
2
replies
259
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
7 days ago • updated 4 days ago BioinfGuru ▴ 30
1
vote
3
replies
257
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 25 days ago by 42k • written 25 days ago by • 0
3
votes
3
replies
254
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 28 days ago by • 0
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
241
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 29 days ago by ★ 4.0k • written 4 weeks ago by ▴ 10
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
1
vote
3
replies
240
views
Different Shrunk Log2FC according with reference
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 20
0
votes
3
replies
236
views
Couldn't connect to server while using "pathways"
graphite
updated 14 days ago by 42k • written 15 days ago by • 0
2
votes
2
replies
236
views
fgsea significant result
fgsea
16 days ago • updated 15 days ago Chris ▴ 10
1
vote
4
replies
234
views
minfi::read.metharray.exp
minfiData minfi
updated 27 days ago by ▴ 780 • written 28 days ago by • 0
2
votes
5
replies
231
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db Bioconductor
5 days ago • updated 4 days ago Patadù ▴ 10
0
votes
3
replies
230
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2 PCAtools
updated 24 days ago by 42k • written 26 days ago by • 0
0
votes
2
replies
225
views
Visium RNA
metaMSdata
written 8 weeks ago by • 0
1
vote
2
replies
218
views
Improving the design matrices vignette in RNAseq123
RNAseq123
29 days ago • updated 15 days ago Lluís Revilla Sancho ▴ 730
0
votes
2
replies
217
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
1
vote
2
replies
208
views
Citation for edgeR user guide
edgeR
written 27 days ago by ▴ 30
0
votes
3
replies
204
views
ChAMP installation issue
Cha ChAMP
8 days ago • updated 7 days ago e1271094 • 0
1
vote
1
reply
195
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 17 days ago by ▴ 10
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 28 days ago by • 0
0
votes
3
replies
190
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 20 days ago by ★ 1.9k • written 4 weeks ago by • 0
2
votes
1
reply
189
views
minfi latest update for EPIC V2 chip
minfi minfiDataEPIC
updated 14 days ago by 66k • written 14 days ago by • 0
0
votes
1
reply
187
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
174 results • Page 2 of 4
Recent ...
Replies
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
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.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
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?
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