2
votes
2
replies
15k
views
Seurat/DESeq2 - single cell RNA-seq differential expression
seurat deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
3
votes
2
replies
1.5k
views
numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
1
vote
3
replies
1.4k
views
Filtering the expression values of a gene from GEO
GEO microarray
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 20
1
vote
0
replies
1.5k
views
Evaluating Hub genes in WGCNA and role of using Signed network
rnaseq WGCNA
7.4 years ago dorothy.jrobbert ▴ 30
0
votes
0
replies
886
views
Do my MA-plots look fine?
ma-plot
7.4 years ago vincentpailler • 0
2
votes
1
reply
863
views
DESeq2 - Three Sample Analysis
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
votes
4
replies
1.5k
views
DESeq2 on two groups
deseq2 group
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
votes
2
replies
2.2k
views
Building linear model (age effect on gene expression)
bioconductor ALL linear model
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
0
votes
5
replies
2.2k
views
Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for slot rowRanges GenomicRangesORGRangesList
deseq2 plotCounts rowRanges
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 50
2
votes
2
replies
753
views
EdgeR Multivariate Analysis question
edger limma
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
2
votes
3
replies
3.4k
views
org.Mm.eg.db gives wrong symbol for MT genes
org.mm.eg.db
12.4 years ago • updated 7.4 years ago Gordon Smyth 53k
0
votes
3
replies
2.5k
views
PureCN: Error in plot.window(...) : need finite 'ylim' values
PureCN
7.6 years ago • updated 7.4 years ago twtoal ▴ 10
3
votes
2
replies
2.4k
views
Installing GEOQuery failed with conda
geoquery anaconda libxml2
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 10
0
votes
0
replies
1.7k
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM samtools pairwisealignment alignment blastn
7.4 years ago ktehmsen • 0
1
vote
6
replies
1.8k
views
Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
ragene20sttranscriptcluster.db
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 40
1
vote
1
reply
622
views
how to run replicates at different time points
limma
updated 7.4 years ago by ★ 29k • written 7.4 years ago by • 0
1
vote
2
replies
2.1k
views
SYMBOL is not the official MGI gene symbol?
org.mm.eg.db annotationdbi
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 20
0
votes
6
replies
2.0k
views
Rsamtools undefined symbol: gzopen64
Rsamtools gzopen64 zlib
updated 7.4 years ago by 25k • written 7.4 years ago by • 0
0
votes
3
replies
2.1k
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
7.4 years ago jbar3141 • 0
1
vote
1
reply
793
views
DESeq2 for ChIP-seq
deseq2 diffbind
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
votes
2
replies
1.6k
views
Ensembl sheep dataset in biomaRt
ensembl biomart oaries
updated 7.4 years ago by ★ 6.6k • written 7.4 years ago by • 0
0
votes
7
replies
3.3k
views
ExperimentHub wackiness (which breaks packages that depend upon experimentHub-provided *data pkgs)
experimenthub
updated 7.4 years ago by 25k • written 7.4 years ago by ★ 4.2k
0
votes
1
reply
2.1k
views
Install Bioconductor package locally/temporarily
R rstudio package installation
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Installation of package 'FDb.InfiniumMethylation.hg19' fails
bioconductor fdb.infiniummethylation.hg19 edger
7.4 years ago m.nabais • 0
5
votes
7
replies
4.4k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Obtaining gene expression value for a list of genes
gene expression
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 20
0
votes
1
reply
1.7k
views
question about getGEO function
geoquery
7.4 years ago maryam.sabet • 0
0
votes
0
replies
1.1k
views
Assessing goodness of fit of a limma model fitted to microarray data
limma microarray goodness of fit
7.4 years ago rubi ▴ 110
1
vote
5
replies
1.8k
views
CRImage createTrainingSet package is not available to install
classification segmentation cell types image analysis crimage
7.4 years ago Jenny.chien • 0
3
votes
7
replies
1.7k
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2 deseq
7.4 years ago blastzone.heimerdinger ▴ 20
4
votes
2
replies
3.3k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 7.4 years ago by ★ 13k • written 7.4 years ago by ▴ 60
1
vote
2
replies
2.7k
views
How to select a specific onthology after runing enrichGO for all 3 onthology
enrichGO clusterprofiler
7.4 years ago MAP ▴ 10
0
votes
4
replies
1.7k
views
how do compare with DESeq2
deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
8
replies
2.9k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
1
reply
806
views
Cultivar+Time+Treatment study in Deseq2
bioconductor deseq2
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
1
vote
2
replies
1.4k
views
I am unable to use Rsubread. Thank you in advance.
rsubread
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
0
votes
1
reply
2.0k
views
Finding/Understanding Affy 6.0 Annotation File
affy affymetrix microarray SNP
7.4 years ago CantExitVIM ▴ 10
2
votes
4
replies
1.6k
views
Homo.sapiens package: Some genes are not found
homo.sapiens
7.4 years ago Vang Le ▴ 80
0
votes
2
replies
1.5k
views
ChipQCreport coverage plot failure?
ChipQC chipqcreport
7.4 years ago tapio.envall • 0
2
votes
4
replies
1.1k
views
Compare in cont.matrix part
microarray R
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
8
votes
6
replies
1.8k
views
Limma weights, non-specific interactions
limma nonspecific filtering weight
updated 7.4 years ago by 53k • written 7.5 years ago by ▴ 20
0
votes
2
replies
1.0k
views
Error: the "phase" metadata column must contain 0, 1, or 2, for all the CDS features
genomicranges
7.4 years ago bbrink • 0
0
votes
0
replies
1.3k
views
BiSeq: Read in Relative Methylation data from CCLE
biseq ccle
7.4 years ago spr ▴ 10
1
vote
3
replies
1.2k
views
Problems with Organism.dplyr
organism.dplyr
updated 7.4 years ago by 25k • written 7.4 years ago by 68k
1
vote
3
replies
1.4k
views
remove NAs values from gset
microarray R
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
3
votes
3
replies
1.9k
views
Gaia results including negative widths
gaia genomicranges iranges
updated 7.4 years ago by ▴ 40 • written 7.4 years ago by ▴ 10
0
votes
8
replies
5.0k
views
DESeq2: handling NA values in colData
deseq2 coldata NA
updated 17 months ago by 43k • written 7.5 years ago by ▴ 170
3
votes
1
reply
1.2k
views
DESeq2: Handling batch effects with only one control replicate coming from another batch
deseq2 rna-seq
updated 7.4 years ago by 43k • written 7.5 years ago by • 0
0
votes
2
replies
1.7k
views
R biomaRt : listDatasets issue
biomart
updated 7.4 years ago by ★ 6.6k • written 7.5 years ago by • 0
4
votes
2
replies
9.6k
views
How to export enrichGO results for future visualization with barplot, dotplot, emapplot...
clusterprofiler enrichGO barplot dotplot
7.4 years ago MAP ▴ 10
46,726 results • Page 253 of 935
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Awards • All
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to nromerov • 0
Popular Question to Thomas Girke ★ 1.7k
Teacher to Gordon Smyth 53k
Popular Question to Stephanie M. Gogarten ▴ 890
Locations • All
WEHI, Melbourne, Australia, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Chile, 4 hours ago
The city by the bay, 5 hours ago
Traffic: 951 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