0
votes
7
replies
436
views
DESeq filtering specific to contrasts
DESeq2
updated 24 days ago by 42k • written 12 weeks ago by • 0
2
votes
9
replies
411
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 18 days ago by 65k • written 18 days ago by • 0
3
votes
10
replies
389
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 3 days ago by 65k • written 6 days ago by • 0
1
vote
2
replies
375
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 9 days ago by 50k • written 9 days ago by • 0
0
votes
8
replies
369
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 18 days ago by ★ 1.4k • written 20 days ago by • 0
1
vote
3
replies
359
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 28 days ago by 50k • written 4 weeks ago by • 0
3
votes
3
replies
358
views
permutation test in edgeR
rna-seq edgeR
updated 22 days ago by 50k • written 5 weeks ago by • 0
1
vote
4
replies
348
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago winwater0928 • 0
1
vote
7
replies
343
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
18 days ago • updated 17 days ago pl23 • 0
1
vote
2
replies
339
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
5 weeks ago • updated 9 days ago Kim • 0
0
votes
7
replies
338
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
26 days ago • updated 20 days ago hortense96 • 0
2
votes
3
replies
334
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
28 days ago • updated 27 days ago daniel.carbajo • 0
0
votes
4
replies
327
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 1 day ago by • 0 • written 12 days ago by ▴ 70
3
votes
1
reply
320
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 days ago by 42k • written 20 days ago by ▴ 40
1
vote
0
replies
316
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
24 days ago BioinfGuru ▴ 30
0
votes
5
replies
311
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 19 days ago by 65k • written 22 days ago by • 0
2
votes
7
replies
296
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
5 days ago • updated 2 days ago sajadahmad41454 • 0
2
votes
5
replies
290
views
get BM error
ensembldb
updated 19 days ago by 65k • written 19 days ago by • 0
1
vote
0
replies
289
views
News: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition Awards Bioconductor Bioc204
7 weeks ago • updated 4 days ago shepherl 3.9k
5
votes
3
replies
287
views
Log-cpm values from limma
limma edgeR RNASeq
updated 3 days ago by 50k • written 25 days ago by • 0
0
votes
3
replies
284
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by 42k • written 12 days ago by • 0
0
votes
4
replies
281
views
DEG with low counts
DESeq2
updated 24 days ago by 42k • written 29 days ago by • 0
1
vote
3
replies
279
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by ★ 4.1k • written 12 days ago by • 0
0
votes
3
replies
272
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 25 days ago by ▴ 850 • written 4 weeks ago by • 0
0
votes
2
replies
268
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
6 weeks ago • updated 24 days ago isaac.vock • 0
1
vote
2
replies
267
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
12 days ago • updated 11 days ago Yveto • 0
0
votes
3
replies
262
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 13 days ago by 65k • written 14 days ago by • 0
0
votes
2
replies
260
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
20 days ago • updated 18 days ago shuwangxinze1996 • 0
0
votes
6
replies
258
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 days ago by ★ 1.4k • written 10 days ago by ▴ 130
3
votes
4
replies
257
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 5 days ago by 50k • written 7 days ago by ▴ 10
1
vote
4
replies
257
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 21 days ago by 65k • written 25 days ago by • 0
3
votes
3
replies
256
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 14 days ago by ★ 4.1k • written 14 days ago by ▴ 10
0
votes
4
replies
256
views
Minfi - estimatecellscount
min minfi
updated 14 days ago by 65k • written 6 weeks ago by • 0
0
votes
1
reply
254
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 13 days ago by 65k • written 13 days ago by • 0
2
votes
5
replies
251
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 18 days ago by 65k • written 19 days ago by • 0
1
vote
2
replies
250
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 24 days ago Weiqian ▴ 10
0
votes
4
replies
248
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
26 days ago • updated 23 days ago lonn • 0
3
votes
4
replies
247
views
Help with error using camera() in limma
CAMERA limma
13 days ago Chris ▴ 10
3
votes
5
replies
242
views
Help with running egsea()
EGSEA
7 days ago • updated 5 days ago Chris ▴ 10
1
vote
3
replies
241
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 17 days ago by 42k • written 18 days ago by • 0
2
votes
2
replies
238
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
6 days ago • updated 12 hours ago zzrammal • 0
3
votes
3
replies
236
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
1
vote
2
replies
228
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
25 days ago Le • 0
0
votes
2
replies
228
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
24 days ago • updated 21 days ago catv • 0
1
vote
3
replies
227
views
Different Shrunk Log2FC according with reference
DESeq2
updated 19 days ago by 42k • written 19 days ago by ▴ 20
3
votes
3
replies
226
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
4 weeks ago • updated 25 days ago jacques.imbert • 0
2
votes
3
replies
225
views
package goseq seems to be not available on the latest version of R
goseq
updated 7 days ago by 50k • written 10 days ago by ▴ 20
2
votes
3
replies
224
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 days ago by ★ 4.1k • written 10 days ago by • 0
0
votes
2
replies
221
views
PCA plot suggestions
DESeq2 PCAtools
updated 17 days ago by 42k • written 18 days ago by • 0
3
votes
2
replies
221
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 21 days ago by ★ 3.9k • written 23 days ago by ▴ 10
192 results • Page 2 of 4
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Comment: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by alex.pico ▴ 20
Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" …
Comment: ChipQC 'names' attribute [9] must be the same length as the vector [2]' by bandconductor • 0
thanks! you have saved me so much time
Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Votes
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
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