2
votes
9
replies
386
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 10 days ago by • 0
1
vote
1
reply
374
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 2 days ago by 50k • written 3 days ago by ▴ 10
1
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3
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348
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 20 days ago by 50k • written 25 days ago by • 0
0
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1
reply
343
views
Gene names from Matrix
BioCor StarBioTrek MatrixGenerics
updated 25 days ago by ▴ 730 • written 7 months ago by • 0
0
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8
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342
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 10 days ago by ★ 1.3k • written 12 days ago by • 0
0
votes
6
replies
337
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
334
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permutation test in edgeR
rna-seq edgeR
updated 14 days ago by 50k • written 27 days ago by • 0
2
votes
3
replies
325
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
20 days ago • updated 19 days ago daniel.carbajo • 0
1
vote
7
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319
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
10 days ago • updated 9 days ago pl23 • 0
1
vote
4
replies
318
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 9 days ago winwater0928 • 0
1
vote
2
replies
317
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
0
votes
7
replies
317
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
18 days ago • updated 12 days ago hortense96 • 0
0
votes
4
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309
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Help with design.matrix
limma
4 weeks ago • updated 29 days ago andrea.rodriguez-martinez13 • 0
3
votes
1
reply
308
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by 41k • written 12 days ago by ▴ 40
0
votes
5
replies
297
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Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 11 days ago by 65k • written 14 days ago by • 0
1
vote
2
replies
290
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
280
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
16 days ago BioinfGuru ▴ 30
3
votes
6
replies
270
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
24 days ago nhaus ▴ 30
0
votes
4
replies
268
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DEG with low counts
DESeq2
updated 16 days ago by 41k • written 21 days ago by • 0
2
votes
5
replies
258
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get BM error
ensembldb
updated 11 days ago by 65k • written 11 days ago by • 0
1
vote
3
replies
256
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 29 days ago by 65k • written 4 weeks ago by • 0
0
votes
2
replies
255
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
5 weeks ago • updated 16 days ago isaac.vock • 0
0
votes
3
replies
254
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 17 days ago by ▴ 850 • written 23 days ago by • 0
0
votes
2
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246
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Regressing out batch effects
DESeq2
updated 25 days ago by 41k • written 4 weeks ago by • 0
0
votes
4
replies
245
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Minfi - estimatecellscount
min minfi
updated 6 days ago by 65k • written 5 weeks ago by • 0
0
votes
2
replies
243
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
12 days ago • updated 10 days ago shuwangxinze1996 • 0
1
vote
2
replies
241
views
How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 16 days ago Weiqian ▴ 10
0
votes
3
replies
241
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
2
votes
5
replies
236
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 10 days ago by 65k • written 11 days ago by • 0
0
votes
4
replies
235
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 days ago • updated 15 days ago lonn • 0
1
vote
4
replies
234
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Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 13 days ago by 65k • written 17 days ago by • 0
0
votes
3
replies
232
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 5 days ago by 65k • written 6 days ago by • 0
3
votes
3
replies
227
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by 41k • written 13 days ago by • 0
0
votes
4
replies
224
views
Storing directories inside an ExperimentHub package?
ExperimentHub
25 days ago • updated 24 days ago Tim Barry • 0
3
votes
3
replies
222
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 days ago by ★ 4.1k • written 6 days ago by ▴ 10
0
votes
2
replies
220
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 25 days ago by 41k • written 4 weeks ago by ▴ 30
0
votes
1
reply
219
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 5 days ago by 65k • written 5 days ago by • 0
0
votes
2
replies
218
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
4 days ago • updated 3 days ago Yveto • 0
1
vote
2
replies
216
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
17 days ago Le • 0
3
votes
2
replies
214
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 13 days ago by ★ 3.9k • written 15 days ago by ▴ 10
1
vote
3
replies
213
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 9 days ago by 41k • written 10 days ago by • 0
0
votes
2
replies
212
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
16 days ago • updated 13 days ago catv • 0
1
vote
3
replies
208
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 20
1
vote
4
replies
205
views
minfi::read.metharray.exp
minfiData minfi
updated 11 days ago by ▴ 780 • written 13 days ago by • 0
0
votes
3
replies
204
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by 41k • written 20 days ago by ▴ 20
0
votes
2
replies
203
views
PCA plot suggestions
DESeq2 PCAtools
updated 9 days ago by 41k • written 10 days ago by • 0
3
votes
3
replies
202
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
23 days ago • updated 17 days ago jacques.imbert • 0
0
votes
4
replies
200
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
17 days ago • updated 16 days ago sropri • 0
3
votes
4
replies
196
views
Help with error using camera() in limma
CAMERA limma
5 days ago Chris • 0
0
votes
4
replies
193
views
flowStats Search Error
flowStats
updated 19 days ago by 3.9k • written 19 days ago by • 0
190 results • Page 2 of 4
Recent ...
Replies
Comment: fgsea significant result by Chris • 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons by Michael Love 41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Votes
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
package goseq seems to be not available on the latest version of R
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