0
votes
0
replies
11
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
1 hour ago Anki • 0
0
votes
0
replies
34
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
13 hours ago Blandine • 0
0
votes
0
replies
28
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
1 day ago Vinesh • 0
0
votes
0
replies
39
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
3 days ago Reuben • 0
0
votes
0
replies
27
views
Problem with PCAtool as dependencie
COTAN PCAtools
4 days ago Silvia • 0
0
votes
0
replies
32
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
5 days ago xiaofeiwang18266 ▴ 50
0
votes
0
replies
71
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
9 days ago • updated 8 days ago nurkenber • 0
0
votes
0
replies
74
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
9 days ago GJ • 0
0
votes
1
reply
139
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 9 days ago by 4.1k • written 11 days ago by • 0
0
votes
2
replies
356
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 12 days ago by ▴ 840
0
votes
0
replies
59
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
14 days ago Maggie • 0
0
votes
0
replies
52
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore FlowCytometry FlowCytometryData
16 days ago vpochic • 0
0
votes
0
replies
72
views
Error ("could not find function "EM_estimate"") when running ENmix mpreprocess() on Microsoft Azure
Preprocessing ENmix
18 days ago balf0020 • 0
0
votes
1
reply
328
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 27 days ago by • 0 • written 5 weeks ago by • 0
0
votes
1
reply
165
views
Errors running learn.bn function from Pigengene in windows environment
Pigengene
written 5 weeks ago by • 0
0
votes
0
replies
10
views
Spam: Best Hotels In Maui
prebs
6 weeks ago 2zrcj3448p 0
0
votes
7
replies
801
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
0
votes
0
replies
120
views
Confidence interval contains 0 but p<0.05
MAST
7 weeks ago Adelyn • 0
0
votes
0
replies
122
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData ExperimentHubData
7 weeks ago Edward • 0
1
vote
4
replies
395
views
pathview - multiple states
pathview Pathways KEGG
7 weeks ago Philippine • 0
0
votes
5
replies
404
views
fail to use addPerROIQC in Rmd
stand standR
updated 7 weeks ago by • 0 • written 7 weeks ago by • 0
0
votes
5
replies
440
views
how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
7 weeks ago • updated 4 weeks ago xiaofeiwang198266 • 0
0
votes
1
reply
208
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 7 weeks ago by • 0 • written 7 weeks ago by • 0
0
votes
0
replies
143
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
8 weeks ago David R ▴ 90
0
votes
1
reply
193
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
votes
1
reply
170
views
eRNAs count
RNASeq DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
0
votes
0
replies
153
views
WGCNA module preservation using only adjacency matrix
WGCNA
10 weeks ago yang1641 • 0
0
votes
0
replies
92
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
10 weeks ago Simone • 0
0
votes
2
replies
394
views
installation error for BiocNeighbors package
BiocNeighbors
10 weeks ago 育 • 0
0
votes
0
replies
193
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP ChAMPdata
10 weeks ago elgomez • 0
1
vote
3
replies
475
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 8 weeks ago abadgerw • 0
0
votes
5
replies
686
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 7 weeks ago abadgerw • 0
0
votes
0
replies
154
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
11 weeks ago user_bioinfo • 0
0
votes
0
replies
216
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
11 weeks ago kim • 0
0
votes
0
replies
168
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub GOSemSim rrvgo
11 weeks ago daccar98 • 0
0
votes
0
replies
169
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
11 weeks ago brayas13 • 0
0
votes
0
replies
146
views
export processed data from flowploidy
flowPloidy
11 weeks ago Zdenek Skala • 0
0
votes
0
replies
112
views
Filtering Steps for proActiv Analysis
Transcriptomics proActiv
12 weeks ago LuciaNhu • 0
0
votes
0
replies
161
views
diffbind covariates
DiffBind ATACSeq
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 220
0
votes
0
replies
117
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
12 weeks ago mario_de_manner • 0
0
votes
0
replies
113
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
3 months ago Ibrahim • 0
0
votes
0
replies
122
views
DiffBind subset replicates
DiffBind
3 months ago Haiping • 0
0
votes
0
replies
174
views
Rsubread - sublong function
pacbio sublong Rsubread
3 months ago thomas.heigl.ibk • 0
0
votes
0
replies
148
views
when FOLD>0, which group of sampls increased?
BASiCS
3 months ago Jeffcgen2000 • 0
0
votes
0
replies
153
views
Paired splsda
mixOmics
3 months ago michelafrancesconi8 • 0
0
votes
0
replies
205
views
Background normalization of Diffbind dba.normalize
Normalization DiffBind
3 months ago Young Boqin • 0
0
votes
0
replies
215
views
DMRcate pcutoff setting
EpicV2 DMRcate
3 months ago kitzhu • 0
0
votes
0
replies
205
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
3 months ago Anke • 0
1
vote
1
reply
415
views
WGCNA
DEGselection RNASeqData WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
0
votes
1
reply
227
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel ChIPQC
written 3 months ago by • 0
1,000 results • Page 1 of 20
Recent ...
Replies
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Awards • All
Popular Question to Martin Morgan 25k
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Joseph Fass ▴ 70
Popular Question to Peter Hickey ▴ 750
Popular Question to Gordon Smyth 52k
Locations • All
WEHI, Melbourne, Australia, 56 minutes ago
Australia, 1 hour ago
The city by the bay, 1 hour ago
Japan, 2 hours ago
United States, 3 hours ago
Traffic: 540 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6