1
vote
13
replies
395
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
13 days ago • updated 10 days ago fernanda.backsouza ▴ 10
4
votes
8
replies
391
views
Memory errors using read.bismark?
dmrseq bsseq
updated 16 days ago by ▴ 740 • written 23 days ago by • 0
2
votes
2
replies
386
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
23 days ago • updated 22 days ago Henry ▴ 10
2
votes
9
replies
376
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 9 days ago by 65k • written 9 days ago by • 0
1
vote
3
replies
347
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 days ago by 50k • written 24 days ago by • 0
0
votes
1
reply
342
views
Gene names from Matrix
BioCor StarBioTrek MatrixGenerics
updated 24 days ago by ▴ 730 • written 7 months ago by • 0
0
votes
8
replies
341
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 9 days ago by ★ 1.3k • written 11 days ago by • 0
0
votes
6
replies
334
views
unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 24 days ago by ▴ 180 • written 4 weeks ago by • 0
3
votes
3
replies
331
views
permutation test in edgeR
rna-seq edgeR
updated 13 days ago by 50k • written 26 days ago by • 0
2
votes
3
replies
322
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
19 days ago • updated 18 days ago daniel.carbajo • 0
0
votes
7
replies
315
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
17 days ago • updated 11 days ago hortense96 • 0
1
vote
4
replies
314
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 8 days ago winwater0928 • 0
1
vote
7
replies
309
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
9 days ago • updated 8 days ago pl23 • 0
0
votes
4
replies
307
views
Help with design.matrix
limma
29 days ago • updated 28 days ago andrea.rodriguez-martinez13 • 0
1
vote
2
replies
306
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 1 day ago by 50k • written 1 day ago by • 0
3
votes
1
reply
305
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 40
0
votes
2
replies
296
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
4 weeks ago • updated 29 days ago fer_talavera • 0
0
votes
5
replies
296
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 10 days ago by 65k • written 13 days ago by • 0
1
vote
2
replies
286
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 1 day ago Kim • 0
1
vote
0
replies
279
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
15 days ago BioinfGuru ▴ 30
3
votes
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
23 days ago nhaus ▴ 30
0
votes
4
replies
263
views
DEG with low counts
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
2
votes
5
replies
255
views
get BM error
ensembldb
updated 10 days ago by 65k • written 10 days ago by • 0
0
votes
2
replies
254
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
4 weeks ago • updated 15 days ago isaac.vock • 0
0
votes
3
replies
251
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 16 days ago by ▴ 850 • written 22 days ago by • 0
1
vote
3
replies
247
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
0
votes
2
replies
245
views
Regressing out batch effects
DESeq2
updated 25 days ago by 41k • written 4 weeks ago by • 0
0
votes
4
replies
244
views
Minfi - estimatecellscount
min minfi
updated 5 days ago by 65k • written 5 weeks ago by • 0
0
votes
2
replies
242
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
11 days ago • updated 9 days ago shuwangxinze1996 • 0
1
vote
2
replies
240
views
How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 15 days ago Weiqian ▴ 10
0
votes
3
replies
236
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
17 days ago • updated 14 days ago lonn • 0
2
votes
5
replies
233
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 9 days ago by 65k • written 11 days ago by • 0
1
vote
4
replies
233
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 12 days ago by 65k • written 16 days ago by • 0
1
vote
1
reply
229
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 1 day ago by 50k • written 2 days ago by ▴ 10
0
votes
3
replies
228
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 4 days ago by 65k • written 5 days ago by • 0
1
vote
2
replies
228
views
MethylKit read issue
methylKit
updated 29 days ago by 65k • written 4 weeks ago by • 0
0
votes
4
replies
222
views
Storing directories inside an ExperimentHub package?
ExperimentHub
24 days ago • updated 23 days ago Tim Barry • 0
3
votes
3
replies
221
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 11 days ago by 41k • written 12 days ago by • 0
0
votes
2
replies
219
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 25 days ago by 41k • written 29 days ago by ▴ 30
0
votes
1
reply
216
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 4 days ago by 65k • written 4 days ago by • 0
3
votes
3
replies
215
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 5 days ago by ★ 4.1k • written 5 days ago by ▴ 10
0
votes
2
replies
213
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
4 days ago • updated 3 days ago Yveto • 0
3
votes
2
replies
212
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 12 days ago by ★ 3.9k • written 15 days ago by ▴ 10
0
votes
2
replies
210
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
15 days ago • updated 12 days ago catv • 0
1
vote
2
replies
210
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
16 days ago Le • 0
1
vote
3
replies
208
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 8 days ago by 41k • written 9 days ago by • 0
1
vote
3
replies
206
views
Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by 41k • written 10 days ago by ▴ 20
0
votes
3
replies
204
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 18 days ago by 41k • written 19 days ago by ▴ 20
1
vote
4
replies
202
views
minfi::read.metharray.exp
minfiData minfi
updated 10 days ago by ▴ 780 • written 12 days ago by • 0
198 results • Page 2 of 4
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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