0
votes
4
replies
373
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by • 0 • written 17 days ago by ▴ 70
1
vote
2
replies
372
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
6 weeks ago • updated 15 days ago Kim • 0
3
votes
3
replies
368
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permutation test in edgeR
rna-seq edgeR
updated 27 days ago by 50k • written 5 weeks ago by • 0
2
votes
2
replies
365
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
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7 days ago • updated 2 days ago Matthew Thornton ▴ 360
0
votes
7
replies
363
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 25 days ago hortense96 • 0
1
vote
7
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359
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Math expression in shapeCustom legend in EnhancedVolcano
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23 days ago • updated 22 days ago pl23 • 0
1
vote
4
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357
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
24 days ago • updated 22 days ago winwater0928 • 0
1
vote
0
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352
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Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
29 days ago BioinfGuru ▴ 30
3
votes
1
reply
328
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by 42k • written 25 days ago by ▴ 40
1
vote
0
replies
324
views
News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
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8 weeks ago • updated 4 days ago shepherl 3.9k
0
votes
5
replies
324
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Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 24 days ago by 65k • written 27 days ago by • 0
4
votes
5
replies
319
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
12 days ago • updated 3 days ago Chris ▴ 10
2
votes
5
replies
307
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get BM error
ensembldb
updated 24 days ago by 65k • written 24 days ago by • 0
5
votes
3
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307
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Log-cpm values from limma
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updated 8 days ago by 50k • written 4 weeks ago by • 0
1
vote
3
replies
304
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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 17 days ago by • 0
0
votes
3
replies
302
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
0
votes
6
replies
293
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 14 days ago by ★ 1.4k • written 16 days ago by ▴ 130
0
votes
4
replies
292
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DEG with low counts
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
3
votes
5
replies
291
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Help with running egsea()
EGSEA
12 days ago • updated 10 days ago Chris ▴ 10
1
vote
2
replies
289
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
17 days ago • updated 16 days ago Yveto • 0
2
votes
4
replies
284
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 26 days ago by 65k • written 4 weeks ago by • 0
0
votes
2
replies
283
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
6 weeks ago • updated 29 days ago isaac.vock • 0
3
votes
4
replies
276
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Store output of matchPWM()
biostrings Biostrings
17 days ago • updated 5 days ago mat149 ▴ 70
2
votes
2
replies
275
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
11 days ago • updated 5 days ago zzrammal • 0
0
votes
3
replies
274
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 18 days ago by 65k • written 19 days ago by • 0
3
votes
3
replies
269
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 19 days ago by ★ 4.1k • written 19 days ago by ▴ 10
1
vote
2
replies
267
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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
267
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package goseq seems to be not available on the latest version of R
goseq
updated 12 days ago by 50k • written 15 days ago by ▴ 20
0
votes
4
replies
266
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
2
replies
266
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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
1
vote
2
replies
264
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How to retrieve detailed regression results from deseq2
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5 weeks ago • updated 29 days ago Weiqian ▴ 10
0
votes
4
replies
264
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Minfi - estimatecellscount
min minfi
updated 19 days ago by 65k • written 7 weeks ago by • 0
0
votes
1
reply
262
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 18 days ago by 65k • written 18 days ago by • 0
3
votes
4
replies
261
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Help with error using camera() in limma
CAMERA limma
18 days ago Chris ▴ 10
2
votes
5
replies
258
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 23 days ago by 65k • written 25 days ago by • 0
2
votes
3
replies
254
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 13 days ago by ★ 4.1k • written 15 days ago by • 0
1
vote
3
replies
253
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 22 days ago by 42k • written 23 days ago by • 0
3
votes
3
replies
251
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 25 days ago by 42k • written 26 days ago by • 0
4
votes
9
replies
247
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
0
votes
2
replies
239
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
29 days ago • updated 26 days ago catv • 0
1
vote
3
replies
238
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 days ago by 50k • written 5 days ago by • 0
1
vote
3
replies
236
views
Different Shrunk Log2FC according with reference
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updated 24 days ago by 42k • written 24 days ago by ▴ 20
2
votes
2
replies
235
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
19 days ago Chris ▴ 10
3
votes
2
replies
231
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Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 26 days ago by ★ 4.0k • written 29 days ago by ▴ 10
1
vote
2
replies
231
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
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5 days ago • updated 2 days ago BioinfGuru ▴ 30
1
vote
4
replies
229
views
minfi::read.metharray.exp
minfiData minfi
updated 24 days ago by ▴ 780 • written 26 days ago by • 0
0
votes
2
replies
227
views
PCA plot suggestions
DESeq2 PCAtools
updated 22 days ago by 42k • written 23 days ago by • 0
2
votes
2
replies
226
views
fgsea significant result
fgsea
14 days ago • updated 13 days ago Chris ▴ 10
0
votes
2
replies
224
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 10 hours ago by 42k • written 1 day ago by • 0
0
votes
3
replies
223
views
Couldn't connect to server while using "pathways"
graphite
updated 12 days ago by 42k • written 12 days ago by • 0
177 results • Page 2 of 4
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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…
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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