Post does not exist.
0
votes
2
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277
views
affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 10 hours ago by 68k • written 1 day ago by • 0
0
votes
1
reply
79
views
Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
updated 11 hours ago by 4.1k • written 13 hours ago by ▴ 140
0
votes
0
replies
36
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
1 day ago GT • 0
0
votes
1
reply
383
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 3 days ago by 68k • written 3 days ago by • 0
0
votes
0
replies
29
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins limma formula design
3 days ago Geoff • 0
0
votes
1
reply
427
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Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
updated 3 days ago by 68k • written 4 days ago by • 0
2
votes
2
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823
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
6 days ago • updated 14 hours ago Elizabeth • 0
1
vote
2
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981
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 days ago • updated 5 days ago Luca • 0
0
votes
1
reply
254
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 5 days ago by 68k • written 6 days ago by • 0
1
vote
2
replies
737
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
6 days ago AB ▴ 110
0
votes
1
reply
151
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling RiboSeq
updated 6 days ago by 4.1k • written 6 days ago by • 0
0
votes
4
replies
461
views
Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
11 days ago • updated 9 hours ago Nicholas • 0
0
votes
1
reply
254
views
Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 7 days ago by 68k • written 7 days ago by • 0
0
votes
0
replies
41
views
Simple confidence intervall Gviz
Gviz
7 days ago William • 0
1
vote
3
replies
19k
views
Warning message---BiocManager::install
BiocManager::install
written 3.6 years ago by • 0
0
votes
2
replies
345
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org.Hs.eg.db issue
org.Hs.eg.db
written 9 weeks ago by • 0
0
votes
2
replies
268
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 8 hours ago by 43k • written 8 days ago by ▴ 20
1
vote
2
replies
686
views
Differential expression of proteins using somascan data
somascan limma
written 10 days ago by • 0
4
votes
4
replies
863
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
11 days ago • updated 10 days ago Elijah • 0
0
votes
1
reply
212
views
library org.Hs.eg.db failing to install
org.Hs.eg.db
updated 11 days ago by 68k • written 11 days ago by • 0
0
votes
1
reply
163
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 11 days ago by 43k • written 12 days ago by • 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 11 days ago by • 0 • written 23 months ago by • 0
0
votes
2
replies
308
views
Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package
hta20transcriptcluster.db org.Sc.sgd.db HTA2.0 MicroRNAArrayData
11 days ago • updated 10 days ago Yao Lipu • 0
0
votes
1
reply
183
views
Is it possible to model DNA methylation as a dose response in edgeR?
edgeR
updated 13 days ago by 52k • written 13 days ago by • 0
0
votes
0
replies
63
views
DiffBind recommendation on using IgG bams
peakcalling DiffBind
13 days ago Harish • 0
0
votes
1
reply
117
views
myvariant error
myvariant getVariants
updated 13 days ago by 68k • written 14 days ago by • 0
0
votes
2
replies
171
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Conumee2 - CNV.summaryplot()
conumee CopyNumberVariation MethylationAnalysis methylationArrayAnalysis EPICv2manifest
updated 13 days ago by 68k • written 13 days ago by • 0
0
votes
1
reply
137
views
DepMap data mismatch
depmap
updated 13 days ago by 1.6k • written 13 days ago by ▴ 30
0
votes
4
replies
2.3k
views
Significant DMRs in genes with no single significant CpG using limma
DMRcate
updated 9 days ago by • 0 • written 5.6 years ago by • 0
0
votes
3
replies
590
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how many significant figures are there in DESeq2 output
DESeq2
updated 15 days ago by ★ 4.7k • written 16 days ago by ▴ 180
0
votes
0
replies
87
views
News: GSEA in R/Bioconductor course
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17 days ago info ▴ 10
0
votes
2
replies
223
views
graper 1.22 Build is Broken
bug graper offtopic
updated 17 days ago by 4.1k • written 17 days ago by • 0
0
votes
1
reply
84
views
cannot download atena annotation for human
atena
17 days ago Davide • 0
0
votes
4
replies
378
views
orgDB
IlluminaDataTestFiles
updated 6 days ago by • 0 • written 17 days ago by • 0
1
vote
1
reply
583
views
GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct" and "unused arguments (exprsData = as.matrix(rna_seq_sub), gset.idx…
GSVA
updated 17 days ago by ★ 4.7k • written 17 days ago by • 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 12 days ago by • 0 • written 17 days ago by • 0
0
votes
1
reply
186
views
Conumee for EPIC and EPICv2 copy number
conumee CopyNumberVariation MethylationArrayData
17 days ago Adam • 0
0
votes
1
reply
85
views
Spam: '"><svg/onload=prompt(5);>{{7*7}}
org.Sc.sgd.db
18 days ago <iframe onload=alert(document.domain)> 0
0
votes
0
replies
17
views
Spam: <iframe onload=alert(document.domain)>
ncdfFlow MethylSeekR cadd.v1.6.hg38 org.Sc.sgd.db MafDb.1Kgenomes.phase1.GRCh38
18 days ago <iframe onload=alert(document.domain)> 0
0
votes
1
reply
172
views
Problem using locateVariants() from the VariantAnnotation package
VariantAnnotation vari
18 days ago • updated 17 days ago Marco • 0
0
votes
0
replies
44
views
SpliceWiz crashes when I apply filters, need splicing analysis help
alternativeSplicingEvents.hg38 AlternativeSplicing SpliceWiz
18 days ago rachel.a.shoemaker • 0
0
votes
1
reply
195
views
pairedGSEA input files
pairedGSEA
updated 18 days ago by 68k • written 19 days ago by • 0
2
votes
5
replies
975
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
19 days ago • updated 18 days ago picasa1983 • 0
0
votes
1
reply
158
views
TheProcess got Killed
DSS
updated 18 days ago by 68k • written 19 days ago by • 0
3
votes
7
replies
2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 18 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
3
votes
2
replies
425
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 18 days ago by ▴ 40 • written 8 weeks ago by • 0
1
vote
2
replies
1.5k
views
help documentation for keytypes in annotationdbi packages
annotation
updated 18 days ago by ▴ 10 • written 4.4 years ago by • 0
0
votes
1
reply
315
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 20 days ago by 68k • written 20 days ago by • 0
1
vote
1
reply
444
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 21 days ago by ★ 1.4k • written 21 days ago by ▴ 10
0
votes
2
replies
388
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cameraPR() non directional test
CAMERA GeneSetEnrichment
24 days ago • updated 21 days ago Hugo Varet ▴ 80
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Comment: edgeR design between and within subjects by wuwenhui2 • 0
Hi Aaron, Your explanation is very helpful. If having three time points instead of three cell types measured for each patient, using the d…
Comment: Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phy by Daniel • 0
Two things: - PR2 version 5.0 and above have 9 levels and not 8 (up to version 4.14). So the code should be: > ranks.pr2 <- c("domain",…
Comment: Removing UTR from GTF for gene quantification by Michael Love 43k
Yes, we need to discourage tagging software packages arbitrarily on Bioconductor support site. This sends emails to the package maintainers…
Comment: Using tximport for kallisto aligned TOIL data by Nicholas • 0
Great, thanks. I have the transcriptome version and the corresponding GTF file for the ENSEMBL transcriptome version. Is there a way to do …
Answer: affy::rma results doesn't match with ncbi website by James W. MacDonald 68k
Please note that RMA is a method intended to normalize and summarize a set of samples rather than a single sample (it doesn't make much sen…
Votes
Comment: Identifying potentially associated gene set to drug response using GSVA
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
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