4
votes
9
replies
452
views
Memory errors using read.bismark?
dmrseq bsseq
4 weeks ago • updated 3 days ago Juan Higareda • 0
2
votes
13
replies
451
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
19 days ago • updated 16 days ago fernanda.backsouza ▴ 10
4
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6
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448
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FilterByExpr low counts with small sample size
edgeR
23 days ago • updated 18 days ago Jonathan ▴ 10
5
votes
6
replies
444
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 28 days ago by ★ 4.1k • written 4 weeks ago by ▴ 30
0
votes
7
replies
434
views
DESeq filtering specific to contrasts
DESeq2
updated 21 days ago by 42k • written 12 weeks ago by • 0
2
votes
9
replies
406
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 15 days ago by 65k • written 16 days ago by • 0
2
votes
2
replies
397
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
29 days ago • updated 28 days ago Henry ▴ 10
0
votes
8
replies
362
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 16 days ago by ★ 1.4k • written 17 days ago by • 0
1
vote
2
replies
360
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 7 days ago by 50k • written 7 days ago by • 0
1
vote
3
replies
356
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 26 days ago by 50k • written 4 weeks ago by • 0
3
votes
3
replies
354
views
permutation test in edgeR
rna-seq edgeR
updated 20 days ago by 50k • written 4 weeks ago by • 0
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
17 days ago • updated 15 days ago winwater0928 • 0
1
vote
7
replies
341
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
15 days ago • updated 14 days ago pl23 • 0
1
vote
2
replies
333
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
5 weeks ago • updated 7 days ago Kim • 0
2
votes
3
replies
333
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
26 days ago • updated 25 days ago daniel.carbajo • 0
0
votes
7
replies
332
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
24 days ago • updated 18 days ago hortense96 • 0
3
votes
1
reply
319
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 17 days ago by 42k • written 17 days ago by ▴ 40
1
vote
0
replies
310
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
22 days ago • updated 21 days ago BioinfGuru ▴ 30
0
votes
5
replies
308
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 17 days ago by 65k • written 19 days ago by • 0
3
votes
10
replies
302
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 1 day ago by 65k • written 3 days ago by • 0
3
votes
6
replies
289
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
4 weeks ago • updated 29 days ago nhaus ▴ 30
2
votes
5
replies
283
views
get BM error
ensembldb
updated 16 days ago by 65k • written 17 days ago by • 0
0
votes
4
replies
280
views
DEG with low counts
DESeq2
updated 22 days ago by 42k • written 26 days ago by • 0
0
votes
3
replies
270
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 9 days ago by 42k • written 10 days ago by • 0
5
votes
3
replies
270
views
Log-cpm values from limma
limma edgeR RNASeq
updated 1 day ago by 50k • written 23 days ago by • 0
1
vote
0
replies
268
views
News: Nominations for Bioconductor Awards 2024! Deadline May 15
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7 weeks ago • updated 2 days ago shepherl 3.9k
0
votes
3
replies
268
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 22 days ago by ▴ 850 • written 29 days ago by • 0
0
votes
2
replies
266
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
5 weeks ago • updated 21 days ago isaac.vock • 0
1
vote
3
replies
264
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 3 days ago by ★ 4.1k • written 9 days ago by • 0
0
votes
2
replies
259
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
18 days ago • updated 16 days ago shuwangxinze1996 • 0
0
votes
3
replies
258
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 10 days ago by 65k • written 11 days ago by • 0
1
vote
2
replies
255
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
10 days ago • updated 9 days ago Yveto • 0
0
votes
4
replies
255
views
Minfi - estimatecellscount
min minfi
updated 12 days ago by 65k • written 6 weeks ago by • 0
1
vote
4
replies
253
views
Error EPICv2 ChAMP
ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP
updated 18 days ago by 65k • written 22 days ago by • 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 15 days ago by 65k • written 17 days ago by • 0
1
vote
2
replies
250
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 21 days ago Weiqian ▴ 10
3
votes
3
replies
250
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 12 days ago by ★ 4.1k • written 12 days ago by ▴ 10
0
votes
6
replies
248
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 7 days ago by ★ 1.4k • written 8 days ago by ▴ 130
0
votes
4
replies
247
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
24 days ago • updated 21 days ago lonn • 0
0
votes
1
reply
246
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 10 days ago by 65k • written 11 days ago by • 0
3
votes
4
replies
239
views
Help with error using camera() in limma
CAMERA limma
10 days ago Chris • 0
3
votes
4
replies
237
views
Method to find pathways different between 2 groups
fgsea GSVA CAMERA
updated 3 days ago by 50k • written 5 days ago by • 0
1
vote
3
replies
237
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 15 days ago by 42k • written 15 days ago by • 0
3
votes
3
replies
235
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
4
replies
234
views
Storing directories inside an ExperimentHub package?
ExperimentHub
4 weeks ago • updated 29 days ago Tim Barry • 0
2
votes
7
replies
232
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
3 days ago • updated 3 hours ago sajadahmad41454 • 0
1
vote
2
replies
227
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
23 days ago • updated 22 days ago Le • 0
1
vote
3
replies
226
views
Different Shrunk Log2FC according with reference
DESeq2
updated 17 days ago by 42k • written 17 days ago by ▴ 20
0
votes
2
replies
223
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
21 days ago • updated 19 days ago catv • 0
3
votes
3
replies
222
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
29 days ago • updated 23 days ago jacques.imbert • 0
197 results • Page 2 of 4
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Answer: SingleR Label.Ont by Denis • 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
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