2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 days ago by 65k • written 22 days ago by • 0
1
vote
2
replies
396
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 13 days ago by 50k • written 14 days ago by • 0
0
votes
8
replies
381
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 22 days ago by ★ 1.4k • written 24 days ago by • 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
1
vote
2
replies
366
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
6 weeks ago • updated 14 days ago Kim • 0
0
votes
4
replies
365
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 5 days ago by • 0 • written 16 days ago by ▴ 70
0
votes
7
replies
360
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 24 days ago hortense96 • 0
2
votes
7
replies
357
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
9 days ago • updated 6 days ago sajadahmad41454 • 0
1
vote
7
replies
355
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
22 days ago • updated 21 days ago pl23 • 0
1
vote
4
replies
355
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago winwater0928 • 0
1
vote
0
replies
346
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
28 days ago BioinfGuru ▴ 30
2
votes
2
replies
328
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
5 days ago • updated 1 day ago Matthew Thornton ▴ 360
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 23 days ago by 42k • written 24 days ago by ▴ 40
0
votes
5
replies
324
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 23 days ago by 65k • written 26 days ago by • 0
1
vote
0
replies
318
views
News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition Awards Bioconductor Bioc204
8 weeks ago • updated 3 days ago shepherl 3.9k
4
votes
5
replies
313
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
11 days ago • updated 2 days ago Chris ▴ 10
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
2
votes
5
replies
303
views
get BM error
ensembldb
updated 23 days ago by 65k • written 23 days ago by • 0
1
vote
3
replies
302
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by ★ 4.1k • written 16 days ago by • 0
0
votes
3
replies
300
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
0
votes
4
replies
291
views
DEG with low counts
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
1
vote
2
replies
287
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
16 days ago • updated 15 days ago Yveto • 0
3
votes
5
replies
285
views
Help with running egsea()
EGSEA
11 days ago • updated 9 days ago Chris ▴ 10
0
votes
6
replies
285
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 13 days ago by ★ 1.4k • written 15 days ago by ▴ 130
0
votes
2
replies
281
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
6 weeks ago • updated 28 days ago isaac.vock • 0
2
votes
4
replies
279
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 25 days ago by 65k • written 29 days ago by • 0
0
votes
3
replies
279
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 29 days ago by ▴ 850 • written 5 weeks ago by • 0
0
votes
3
replies
273
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 17 days ago by 65k • written 18 days ago by • 0
2
votes
2
replies
268
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
10 days ago • updated 4 days ago zzrammal • 0
3
votes
4
replies
267
views
Store output of matchPWM()
biostrings Biostrings
16 days ago • updated 3 days ago mat149 ▴ 70
3
votes
3
replies
266
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 days ago by ★ 4.1k • written 18 days ago by ▴ 10
0
votes
2
replies
264
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
24 days ago • updated 22 days ago shuwangxinze1996 • 0
0
votes
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 27 days ago lonn • 0
1
vote
2
replies
262
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 28 days ago Weiqian ▴ 10
0
votes
4
replies
262
views
Minfi - estimatecellscount
min minfi
updated 18 days ago by 65k • written 7 weeks ago by • 0
2
votes
3
replies
261
views
package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by 50k • written 14 days ago by ▴ 20
0
votes
1
reply
261
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 17 days ago by 65k • written 17 days ago by • 0
3
votes
4
replies
260
views
Help with error using camera() in limma
CAMERA limma
17 days ago Chris ▴ 10
2
votes
5
replies
258
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 22 days ago by 65k • written 23 days ago by • 0
1
vote
2
replies
254
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
8 days ago • updated 7 days ago Dylan.Sheerin • 0
2
votes
3
replies
252
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
1
vote
3
replies
252
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 21 days ago by 42k • written 22 days ago by • 0
3
votes
3
replies
250
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by 42k • written 25 days ago by • 0
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
5 weeks ago • updated 29 days ago jacques.imbert • 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
28 days ago • updated 25 days ago catv • 0
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by 42k • written 23 days ago by ▴ 20
1
vote
2
replies
233
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
29 days ago Le • 0
2
votes
2
replies
232
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago Chris ▴ 10
3
votes
2
replies
229
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 25 days ago by ★ 4.0k • written 28 days ago by ▴ 10
1
vote
4
replies
228
views
minfi::read.metharray.exp
minfiData minfi
updated 23 days ago by ▴ 780 • written 25 days ago by • 0
192 results • Page 2 of 4
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
United States, 5 minutes ago
United States, 5 minutes ago
United States, 21 minutes ago
United States, 23 minutes ago
EMBL Heidelberg, 24 minutes ago
Traffic: 671 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6