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
0
votes
0
replies
1.9k
views
PhD / PostDoc positions in Innsbruck, Austria
Microarray
GO
Cancer
Leukemia
Microarray
GO
Cancer
Leukemia
16.9 years ago
Johannes Rainer
▴ 80
0
votes
3
replies
1.5k
views
biomart package - error querying for ensembl gene ID in snp mart
SNP
biomaRt
SNP
biomaRt
16.9 years ago
martin sikora
▴ 60
0
votes
3
replies
1.7k
views
limma - interpreting factorial design
limma
limma
updated 16.9 years ago by
Björn Usadel
▴ 250 • written 16.9 years ago by
john seers IFR
▴ 810
0
votes
0
replies
1.2k
views
GenomeGraphs plot colours (bug?)
graph
GenomeGraphs
graph
GenomeGraphs
16.9 years ago
Tim Rayner
▴ 270
0
votes
3
replies
2.4k
views
cannot access annotation from ExpressionSet in Bioc-Devel
Annotation
GO
Biobase
limma
Annotation
GO
Biobase
limma
updated 16.9 years ago by
john seers IFR
▴ 810 • written 16.9 years ago by
Mark W Kimpel
▴ 830
0
votes
1
reply
1.4k
views
How to install chipseq package
ChIPSeq
chipseq
ChIPSeq
chipseq
updated 16.9 years ago by
Patrick Aboyoun
★ 1.6k • written 16.9 years ago by
Yuan Hao
▴ 90
0
votes
0
replies
2.0k
views
Mapping GO term ID to Illumina probe ID for Illumina gene expression data
GO
probe
GO
probe
16.9 years ago
Pan Du
★ 1.2k
0
votes
2
replies
1.2k
views
Mapping GO term ID to Illumina probe ID for Illumina gene expression data
GO
probe
GO
probe
updated 16.9 years ago by
Sean Davis
21k • written 16.9 years ago by
affy snp
▴ 640
0
votes
0
replies
1.0k
views
Help: Problems with LmFit
Cancer
limma
Cancer
limma
16.9 years ago
julin@aecom.yu.edu
▴ 80
0
votes
1
reply
852
views
shortReads
updated 16.9 years ago by
Martin Morgan
25k • written 16.9 years ago by
Lana Schaffer
★ 1.3k
0
votes
1
reply
1.2k
views
RefPlus error
RefPlus
RefPlus
updated 16.9 years ago by
Harbron, Chris
▴ 20 • written 16.9 years ago by
Christian Ruckert
▴ 170
0
votes
3
replies
7.6k
views
org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Cancer
Homo sapiens
convert
Cancer
Homo sapiens
convert
updated 16.9 years ago by
Seraya Maouche
▴ 10 • written 16.9 years ago by
Tim Smith
★ 1.1k
0
votes
2
replies
2.3k
views
Analysing Agilent microarray data
Microarray
Microarray
updated 16.9 years ago by
Pedro López Romero
▴ 360 • written 16.9 years ago by
Christian Brière
▴ 90
0
votes
13
replies
3.6k
views
two color arrays normalization
limma
limma
updated 16.9 years ago by
Jenny Drnevich
★ 2.0k • written 16.9 years ago by
Giusy Della Gatta
▴ 110
0
votes
0
replies
834
views
Keep getting warning messages of package 'XYZ' was built under R version 2.8.1
16.9 years ago
Patrick Aboyoun
★ 1.6k
0
votes
0
replies
867
views
Keep getting warning messages of package 'XYZ' was builtunder R version 2.8.1
16.9 years ago
michael watson IAH-C
★ 3.4k
0
votes
3
replies
2.0k
views
Keep getting warning messages of package 'XYZ' was built under R version 2.8.1
updated 16.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 16.9 years ago by
Daren Tan
▴ 190
0
votes
1
reply
1.1k
views
Illustrator import
updated 16.9 years ago by
Cei Abreu-Goodger
▴ 830 • written 16.9 years ago by
Sim, Fraser
▴ 350
0
votes
0
replies
814
views
normalizing with control spots
Normalization
limma
Normalization
limma
16.9 years ago
alison waller
▴ 180
0
votes
3
replies
1.4k
views
IRanges: find containment and not just overlap
IRanges
IRanges
updated 16.9 years ago by
Michael Lawrence
▴ 620 • written 16.9 years ago by
Elizabeth Purdom
▴ 210
0
votes
0
replies
840
views
Suggestions for a library/plate sorting algorithm
16.9 years ago
Paul Leo
▴ 970
0
votes
1
reply
1.0k
views
CSHL course
GO
GO
16.9 years ago
John Zhang
★ 2.9k
0
votes
1
reply
1.0k
views
Error with GeneSetCollection - Pfam or Chrloc
Annotation
hgu95a
Annotation
hgu95a
updated 16.9 years ago by
Martin Morgan
25k • written 16.9 years ago by
James Wagner
▴ 30
0
votes
2
replies
1.4k
views
Draft paper submission deadline extended: BCBGC-09
16.9 years ago
John Edward
▴ 80
0
votes
8
replies
2.5k
views
Annotation for Medicago array (Affy)
updated 16.9 years ago by
Ana Conesa
▴ 340 • written 16.9 years ago by
Guido Hooiveld
★ 4.1k
0
votes
1
reply
1.0k
views
BioC 2.2 release update.packages error
updated 16.9 years ago by
Patrick Aboyoun
★ 1.6k • written 16.9 years ago by
Elliot Kleiman
▴ 150
0
votes
0
replies
638
views
General Dentists Listing for the United States
16.9 years ago
Eli O Shaw
▴ 10
0
votes
0
replies
1.1k
views
MBNI Custom CDF Announcement
cdf
probe
Vega
cdf
probe
Vega
16.9 years ago
Manhong Dai
▴ 200
0
votes
0
replies
1.6k
views
qPCR NEWS - February 2009
qPCR
Normalization
PROcess
microRNA
qPCR
Normalization
PROcess
microRNA
16.9 years ago
qPCR Platform - the reference in real-t…
▴ 170
0
votes
11
replies
2.7k
views
...another question about using weights on microarray analysis
Microarray
limma
ASSIGN
Microarray
limma
ASSIGN
16.9 years ago
Erika Melissari
▴ 250
0
votes
2
replies
2.8k
views
How to use GOSlim with GOstats
GOstats
GOstats
updated 16.9 years ago by
Marc Carlson
★ 7.2k • written 16.9 years ago by
Iain Wallace
▴ 50
0
votes
5
replies
1.6k
views
edgeR and sagenhaft
SAGE
GO
edgeR
SAGE
GO
edgeR
16.9 years ago
Naomi Altman
★ 6.0k
0
votes
0
replies
772
views
understanding contrast matrix
16.9 years ago
hemant ritturaj
▴ 150
0
votes
0
replies
653
views
Are you Lost on the Marketing Concept -
PROcess
PROcess
16.9 years ago
Leslie Jolliff
▴ 10
0
votes
0
replies
798
views
Boston bioconductor training registration now closed
16.9 years ago
Vincent J. Carey, Jr.
6.7k
0
votes
1
reply
937
views
Confusing results
Microarray
Microarray
updated 16.9 years ago by
Jenny Drnevich
★ 2.0k • written 16.9 years ago by
hemant ritturaj
▴ 150
0
votes
3
replies
1.6k
views
"Size" in summary() of "hyperGTest()
GO
Category
GO
Category
updated 16.9 years ago by
rgentleman
★ 5.5k • written 16.9 years ago by
Sergei Manakov
▴ 30
0
votes
1
reply
1.0k
views
diferent pvalues for a treatment when other contrasts areremoved from targets file
updated 16.9 years ago by
Agnieszka Zmienko
▴ 50 • written 16.9 years ago by
James W. MacDonald
68k
0
votes
0
replies
970
views
[Fwd: Reporting problem with annotation in biomaRt, Illumina arrays - correction]
Annotation
probe
biomaRt
Annotation
probe
biomaRt
16.9 years ago
Pan Du
★ 1.2k
0
votes
0
replies
1.1k
views
JOB UCSF
Microarray
Microarray
16.9 years ago
mark@biostat.ucsf.edu
▴ 30
0
votes
0
replies
689
views
Reporting problem with annotation in biomaRt, Illumina arrays - correction
Annotation
probe
biomaRt
Annotation
probe
biomaRt
16.9 years ago
Nenad Bartonicek
▴ 20
0
votes
2
replies
1.1k
views
Adding annotations to fit2 - still having problems
Microarray
limma
Microarray
limma
updated 16.9 years ago by
Sean Davis
21k • written 16.9 years ago by
Sally
▴ 250
0
votes
10
replies
2.3k
views
Timecourse package
Microarray
TimeCourse
timecourse
Microarray
TimeCourse
timecourse
updated 16.9 years ago by
Yu Chuan Tai
▴ 440 • written 16.9 years ago by
Priscila Grynberg
▴ 380
0
votes
5
replies
1.6k
views
xps rma() with HuGene-1_0-st-v1 on 64-bit architecture
Annotation
Preprocessing
probe
oligo
xps
Annotation
Preprocessing
probe
oligo
xps
updated 16.9 years ago by
cstrato
★ 3.9k • written 16.9 years ago by
Tim Rayner
▴ 270
0
votes
3
replies
1.3k
views
Adding annotations to fit2
updated 16.9 years ago by
john seers IFR
▴ 810 • written 16.9 years ago by
Sally
▴ 250
0
votes
0
replies
686
views
bioconductor
GO
GO
16.9 years ago
Ayyarappan Bharathi
▴ 20
0
votes
0
replies
813
views
diferent pvalues for a treatment when other contrasts are removed from targets file
16.9 years ago
Agnieszka Zmienko
▴ 50
0
votes
3
replies
1.4k
views
Save rma normalization results for later use
updated 16.9 years ago by
Laurent Gatto
1.6k • written 16.9 years ago by
Christian Ruckert
▴ 170
0
votes
0
replies
894
views
[Fwd: Reporting problem with annotation in biomaRt, Illumina arrays]
Annotation
probe
biomaRt
Annotation
probe
biomaRt
16.9 years ago
Wolfgang Huber
★ 13k
0
votes
1
reply
1.3k
views
Where to download annotation package for Agilent human CGH 44B
Annotation
CGH
Annotation
CGH
updated 16.9 years ago by
Marc Carlson
★ 7.2k • written 16.9 years ago by
Daren Tan
▴ 190
46,726 results • Page
722 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
nromerov
• 0
Popular Question
to
Thomas Girke
★ 1.7k
Teacher
to
Gordon Smyth
53k
Popular Question
to
Stephanie M. Gogarten
▴ 890
Autobiographer
to
Frances Turner
▴ 20
Locations
• All
The city by the bay,
9 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
United States,
1 hour ago
Iran,
3 hours ago
France,
6 hours ago
Traffic: 795 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