Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
R
•
reset
10
votes
10
replies
7.0k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 6 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 4 weeks ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
4
replies
375
views
limma with interaction term
R
biostatistics
limma
Epigenetics
12 weeks ago • updated 10 weeks ago
Jitendra
▴ 10
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
9 months ago
mohammedtoufiq91
▴ 10
7
votes
5
replies
7.0k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 6 months ago by
Ke
• 0 • written 2.0 years ago by
kieran.short
▴ 40
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 11 months ago by
hfbarrerat
• 0 • written 3.2 years ago by
Bethan
• 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 7 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 4 months ago by
Rory Stark
★ 5.2k • written 6.6 years ago by
kyliecode
• 0
0
votes
6
replies
8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler
r
updated 4 months ago by
Guido Hooiveld
★ 3.9k • written 7.3 years ago by
prp291
• 0
0
votes
2
replies
2.1k
views
Creating a qPCRset object from a text file
qPCRset object
nondetects
r
package
txt
updated 6 months ago by
Nat.Nataren
• 0 • written 6.3 years ago by
s.m.may
• 0
3
votes
3
replies
4.7k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 11 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R
oligoClasses
Oligoclass
Bioconductor
Oligo
written 3.2 years ago by
tanya
• 0
22
votes
15
replies
7.5k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 6 months ago by
Marie
▴ 10 • written 2.1 years ago by
Dina
▴ 50
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 7 months ago by
jacorvar
▴ 40 • written 19 months ago by
eraldagjika
▴ 20
1
vote
12
replies
2.4k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 3 months ago by
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
0
votes
10
replies
819
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R
BioMart
biomaRt
5 months ago • updated 9 weeks ago
ScafioRuo
• 0
1
vote
2
replies
613
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl
R
biomaRt
9 months ago
Miguel
• 0
3
votes
4
replies
536
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
0
votes
2
replies
563
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
9 months ago • updated 8 months ago
yr542
• 0
0
votes
3
replies
500
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
updated 4 months ago by
daenerystargaryen56
• 0 • written 5 months ago by
Sitapriya
• 0
0
votes
0
replies
236
views
multipollutant models
statistics
Regression
r
limma
5 months ago
Jitendra
▴ 10
0
votes
0
replies
117
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
9 weeks ago
danalvoronov
▴ 10
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 12 weeks ago by
Gordon Smyth
50k • written 4.8 years ago by
sambunga094
• 0
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG
GAGE
NaN
R
DESeq2
updated 12 months ago by
Rob
• 0 • written 5.5 years ago by
owen.donohoe
• 0
0
votes
1
reply
523
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 10 months ago by
Lluís Revilla Sancho
▴ 730 • written 10 months ago by
Eliza
• 0
29 results • Page
1 of 1
Recent ...
Replies
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
Regardless of whether it agrees with `t.test` or not, the formula given in the original question is correct and yours is not. Your formula …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Awards
• All
Popular Question
to
Gyan Prakash Mishra
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
WouterDeCoster
▴ 130
Scholar
to
Michael Love
42k
Popular Question
to
Malcolm Cook
★ 1.6k
Locations
• All
WEHI, Melbourne, Australia,
2 minutes ago
United States,
11 minutes ago
United States,
15 minutes ago
United States,
33 minutes ago
India,
43 minutes ago
Traffic: 500 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