1
vote
2
replies
398
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 14 days ago by 50k • written 14 days ago by • 0
0
votes
8
replies
383
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 23 days ago by ★ 1.4k • written 24 days ago by • 0
1
vote
2
replies
369
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
6 weeks ago • updated 14 days ago Kim • 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq edgeR
updated 27 days ago by 50k • written 5 weeks ago by • 0
0
votes
4
replies
367
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 6 days ago by • 0 • written 16 days ago by ▴ 70
2
votes
7
replies
364
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
10 days ago • updated 6 days ago sajadahmad41454 • 0
0
votes
7
replies
362
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 25 days ago hortense96 • 0
1
vote
7
replies
357
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
22 days ago • updated 21 days ago pl23 • 0
1
vote
4
replies
356
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
24 days ago • updated 22 days ago winwater0928 • 0
2
votes
2
replies
349
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
6 days ago • updated 1 day ago Matthew Thornton ▴ 360
1
vote
0
replies
348
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
28 days ago BioinfGuru ▴ 30
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 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
321
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
317
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
12 days ago • updated 2 days ago Chris ▴ 10
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 4 weeks ago by • 0
2
votes
5
replies
304
views
get BM error
ensembldb
updated 23 days ago by 65k • written 24 days ago by • 0
1
vote
3
replies
303
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 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 17 days ago by • 0
0
votes
4
replies
292
views
DEG with low counts
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
0
votes
6
replies
291
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 14 days ago by ★ 1.4k • written 15 days ago by ▴ 130
3
votes
5
replies
290
views
Help with running egsea()
EGSEA
11 days ago • updated 10 days ago Chris ▴ 10
1
vote
2
replies
288
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
17 days ago • updated 16 days ago Yveto • 0
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
0
votes
3
replies
281
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 29 days ago by ▴ 850 • written 5 weeks ago by • 0
2
votes
4
replies
280
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
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
3
votes
4
replies
271
views
Store output of matchPWM()
biostrings Biostrings
16 days ago • updated 4 days ago mat149 ▴ 70
2
votes
2
replies
271
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
10 days ago • updated 5 days ago zzrammal • 0
3
votes
3
replies
268
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 days ago by ★ 4.1k • written 19 days ago by ▴ 10
0
votes
2
replies
265
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
25 days ago • updated 23 days ago shuwangxinze1996 • 0
2
votes
3
replies
263
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
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 28 days ago lonn • 0
0
votes
1
reply
262
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 18 days ago by • 0
0
votes
4
replies
262
views
Minfi - estimatecellscount
min minfi
updated 18 days ago by 65k • written 7 weeks ago by • 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
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 24 days ago by • 0
1
vote
2
replies
257
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
9 days ago • updated 8 days ago Dylan.Sheerin • 0
2
votes
3
replies
254
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
253
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
2
replies
235
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago • updated 29 days ago Le • 0
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by 42k • written 24 days ago by ▴ 20
2
votes
2
replies
234
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago Chris ▴ 10
1
vote
3
replies
233
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 3 days ago by 50k • written 4 days ago by • 0
4
votes
9
replies
233
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 1 day ago by ★ 4.1k • written 3 days ago by • 0
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
190 results • Page 2 of 4
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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" …
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
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