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 :
vsn
•
reset
1
vote
0
replies
564
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn
vsn
Normalization
vsn2
Proteomics
15 months ago
Arend
▴ 10
7
votes
3
replies
4.3k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r
limma
voom
vsn
updated 17 months ago by
Gordon Smyth
50k • written 5.1 years ago by
Sebastian Hesse
▴ 70
0
votes
3
replies
2.3k
views
Different PCA results when using rlog and vst transformations
vsn
DESeq2
rlog
BatchEffect
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
Diamond
• 0
0
votes
5
replies
1.1k
views
In need of linear modeling help for differential expression (proteomics)
Proteomics
limma
vsn
updated 2.7 years ago by
Gordon Smyth
50k • written 2.7 years ago by
Chris
• 0
2
votes
3
replies
1.1k
views
one stratum from vsn2
vsn
vsn2
onestratum
updated 3.3 years ago by
Wolfgang Huber
★ 13k • written 3.3 years ago by
pros_vs_chur
• 0
4
votes
4
replies
1.6k
views
change all the negative value into positive value
vsn
3.4 years ago • updated 3.3 years ago
yueli7
▴ 20
4
votes
4
replies
1.5k
views
Where can I use the VSN source code in C++?
vsn
r language
C++
source code
updated 7.2 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.2 years ago by
core_wzw
• 0
1
vote
2
replies
1.2k
views
Bug in vsn2 in package vsn?
vsn
vsn2
updated 7.2 years ago by
Wolfgang Huber
★ 13k • written 7.2 years ago by
Peter Langfelder
★ 3.0k
0
votes
3
replies
2.5k
views
Error: could not find function "normalize.AffyBatch.vsn"
vsn
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
billchenxi
• 0
0
votes
2
replies
1.3k
views
normalize.AffyBatch.vsn not expressed in vsn
software error
vsn
affy
7.4 years ago
Claudio Lottaz
▴ 40
2
votes
1
reply
1.0k
views
vsn package problem
vsn
updated 8.2 years ago by
James W. MacDonald
65k • written 8.2 years ago by
wenbo
• 0
0
votes
3
replies
2.9k
views
error in vsn package
vsn
failure to read documentation error
updated 8.4 years ago by
Wolfgang Huber
★ 13k • written 8.4 years ago by
Angel
▴ 40
1
vote
5
replies
1.5k
views
normalization of a miRNA microarray
normalization
vsn
eximir
microarray
miRNA
updated 8.6 years ago by
Wolfgang Huber
★ 13k • written 8.6 years ago by
alptaciroglu
▴ 50
0
votes
6
replies
2.4k
views
how to use negative controls to obtain scale and offset parameters then to normalize the whole protein microarray data by vsn method
vsn
protein microarray
normalization
scale and offset parameters
8.6 years ago
guojiegina
• 0
3
votes
2
replies
5.6k
views
problem installing "vsn" on debian... gcc: error: unrecognized command line option -fstack-protector-strong
install
vsn
gcc
debian
9.2 years ago
regcl
• 0
5
votes
6
replies
6.3k
views
proper transformation for differential expression in normalized log expression data
tcga
rnaseq
deseq2
vsn
edger
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
rachel.melamed
• 0
0
votes
1
reply
1.3k
views
vsn normalization in Ringo package
Normalization
vsn
Ringo
Normalization
vsn
Ringo
updated 9.7 years ago by
Joern Toedling
▴ 10 • written 9.7 years ago by
Guest User
★ 13k
0
votes
1
reply
1.3k
views
VSN with spike-in probes question
vsn
vsn
updated 9.8 years ago by
Wolfgang Huber
★ 13k • written 9.8 years ago by
Matthew Thornton
▴ 350
0
votes
1
reply
1.3k
views
VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?
vsn
PROcess
xps
vsn
PROcess
xps
updated 10.1 years ago by
Wolfgang Huber
★ 13k • written 10.1 years ago by
Matthew Thornton
▴ 350
0
votes
1
reply
1.3k
views
Statistics questions regarding the use of Ambion ExFold ERCC standards with Affmetrix ST arrays.
Normalization
vsn
graph
Normalization
vsn
graph
updated 10.3 years ago by
James W. MacDonald
65k • written 10.3 years ago by
Matthew Thornton
▴ 350
0
votes
1
reply
2.2k
views
Importing RMA processed data into limma for eBayes
Microarray
Normalization
affy
vsn
limma
PROcess
xps
Microarray
Normalization
affy
vsn
10.3 years ago
Matthew Thornton
▴ 350
0
votes
5
replies
2.2k
views
Single-channel GenePix analysis with Limma (bg correction, normalization, weights)
Microarray
Normalization
vsn
limma
ASSIGN
Microarray
Normalization
vsn
limma
ASSIGN
updated 10.4 years ago by
Gordon Smyth
50k • written 10.5 years ago by
Marcin Jakub Kamiński
▴ 40
0
votes
0
replies
987
views
question about package AgiMicroRna
Normalization
GO
vsn
Normalization
GO
vsn
10.7 years ago
Guest User
★ 13k
0
votes
0
replies
1.6k
views
Bioconductor Digest, Vol 121, Issue 29
miRNA
Annotation
Normalization
Visualization
Clustering
Infrastructure
Cancer
BSgenome
vsn
11.1 years ago
Matthew Thornton
▴ 350
0
votes
6
replies
1.7k
views
Heatmaps for Agilent Single Color 4x44k using limma and vsn.
Annotation
Normalization
vsn
limma
Annotation
Normalization
vsn
limma
updated 11.1 years ago by
James W. MacDonald
65k • written 11.1 years ago by
Cornish, Joseph NIH/NIAID [F]
▴ 50
0
votes
8
replies
2.1k
views
vsn preprocess with oligo package
vsn
oligo
oligoClasses
vsn
oligo
oligoClasses
updated 11.3 years ago by
James W. MacDonald
65k • written 11.3 years ago by
José LÓPEZ
▴ 110
0
votes
3
replies
1.5k
views
Most diff exp genes are up-regulated... can this be true?
Microarray
Normalization
vsn
limma
siggenes
Microarray
Normalization
vsn
limma
siggenes
11.4 years ago
Peter Davidsen
▴ 210
0
votes
2
replies
1.5k
views
normalize.AffyBatch.vsn with reference vsn object
vsn
vsn
updated 12.0 years ago by
Wolfgang Huber
★ 13k • written 12.0 years ago by
R Tagett
▴ 30
0
votes
0
replies
942
views
PLS help: is it sound to normalized highthrouput qPCR arrays using vsn?
qPCR
Normalization
vsn
qPCR
Normalization
vsn
12.0 years ago
Ali Mohammadian
▴ 290
0
votes
0
replies
969
views
Problem with BGandNorm() from the Agi4x44PreProcess package
vsn
Agi4x44PreProcess
vsn
Agi4x44PreProcess
12.0 years ago
marco fabbri
▴ 320
0
votes
1
reply
1.2k
views
using vsn to normalize protein array data
Microarray
vsn
Microarray
vsn
updated 12.6 years ago by
Wolfgang Huber
★ 13k • written 12.6 years ago by
Jabez Wilson
▴ 150
0
votes
1
reply
1.2k
views
Problem with BGandNorm() from the Agi4x44PreProcess package
vsn
vsn
updated 13.0 years ago by
Wolfgang Huber
★ 13k • written 13.0 years ago by
Dick Beyer
★ 1.4k
0
votes
1
reply
1.3k
views
odd limma results?
vsn
limma
vsn
limma
updated 13.3 years ago by
James W. MacDonald
65k • written 13.3 years ago by
David A.
▴ 70
2
votes
4
replies
2.2k
views
limma and minimum fold change
Microarray
vsn
limma
Microarray
vsn
limma
updated 13.4 years ago by
Sean Davis
21k • written 13.4 years ago by
Eva Benito Garagorri
▴ 70
0
votes
1
reply
1.7k
views
Question: How does limma derives its logFC value in two colored arrays?
Yeast
affy
vsn
limma
Yeast
affy
vsn
limma
updated 13.6 years ago by
Sunny Srivastava
▴ 350 • written 13.6 years ago by
Gordon Smyth
50k
0
votes
3
replies
1.5k
views
ChIP-chip sequence bias not removed
Normalization
vsn
Starr
Normalization
vsn
Starr
updated 13.8 years ago by
zacher@lmb.uni-muenchen.de
▴ 50 • written 13.8 years ago by
Edwin Groot
▴ 230
0
votes
4
replies
1.8k
views
gc-rma and vsn normalization for rat microarray data
Microarray
Annotation
Normalization
vsn
bgx
puma
Microarray
Annotation
Normalization
vsn
updated 13.9 years ago by
Benilton Carvalho
★ 4.3k • written 13.9 years ago by
Rainer Tischler
▴ 60
0
votes
0
replies
903
views
duplicate spots
vsn
vsn
13.9 years ago
David
▴ 860
0
votes
1
reply
1.1k
views
No changes between Groups using GeneST Arrays from Affymetrix
GO
vsn
plier
GO
vsn
plier
updated 14.0 years ago by
Mike Walter
▴ 230 • written 14.0 years ago by
Benjamin Otto
▴ 830
0
votes
3
replies
1.1k
views
VSN: minimum number of controls?
Normalization
vsn
Normalization
vsn
updated 14.1 years ago by
Martin Morgan
25k • written 14.1 years ago by
Eric E. Snyder
▴ 20
0
votes
6
replies
1.8k
views
Normalisation of Agilent microRNA arrays using inbuilt controls?
GO
Cancer
vsn
AgiMicroRna
GO
Cancer
vsn
AgiMicroRna
updated 14.2 years ago by
Wei Shi
★ 3.6k • written 14.2 years ago by
Daniel Brewer
★ 1.9k
0
votes
2
replies
1.6k
views
MA plots + dye swap
Normalization
vsn
limma
Normalization
vsn
limma
updated 14.2 years ago by
Claus Mayer
▴ 340 • written 14.2 years ago by
Guido Hooiveld
★ 3.9k
0
votes
2
replies
1.5k
views
vsn and oligo (or xps?) packages for GeneST expression arrays
vsn
oligo
xps
vsn
oligo
xps
updated 14.3 years ago by
cstrato
★ 3.9k • written 14.3 years ago by
Tim Rayner
▴ 270
0
votes
5
replies
2.9k
views
vsn: meanSdPlot + MAlist
Normalization
vsn
limma
convert
Normalization
vsn
limma
convert
updated 14.5 years ago by
Martin Morgan
25k • written 14.5 years ago by
Guido Hooiveld
★ 3.9k
0
votes
11
replies
3.0k
views
Very low P-values in limma
miRNA
Microarray
Normalization
GO
vsn
limma
microRNA
miRNA
Microarray
Normalization
GO
updated 14.5 years ago by
Paul Geeleher
★ 1.3k • written 14.5 years ago by
Gordon Smyth
50k
0
votes
1
reply
914
views
multiple Affy normalization results in single object ?
Biobase
vsn
Biobase
vsn
updated 14.6 years ago by
Martin Morgan
25k • written 14.6 years ago by
Wolfgang RAFFELSBERGER
▴ 140
0
votes
3
replies
1.5k
views
limma's implementation of VSN
Normalization
vsn
limma
Normalization
vsn
limma
updated 14.6 years ago by
Wolfgang Huber
★ 13k • written 14.6 years ago by
Guido Hooiveld
★ 3.9k
0
votes
0
replies
1.3k
views
LIMMA: Why does eBayes expression differ from observed?
Normalization
Preprocessing
probe
vsn
limma
Normalization
Preprocessing
probe
vsn
limma
14.7 years ago
Axel Klenk
★ 1.0k
0
votes
0
replies
937
views
Subject: Re: Normalization of arrays where most of the genes change
Normalization
vsn
limma
Normalization
vsn
limma
15.0 years ago
Alicia Oshlack
▴ 70
0
votes
0
replies
1.0k
views
vsn add-on normalization
Normalization
vsn
Normalization
vsn
15.1 years ago
Markus Schmidberger
▴ 380
50 results • Page
1 of 1
Recent ...
Replies
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Answer: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
Tim Peters
▴ 170
Hi Jose and Russ, Apologies to Jose for not seeing this earlier. Sometimes the loess smoother in the bottom panel will throw this error …
Comment: Trying to use enrichGO
by
fernanda.backsouza
• 0
Sure, I changed it but still NULL G0 <- enrichGO( gene = ortologos_filtrados$Gene.ID, OrgDb = org.Cs.eg.db, keyType = "ENTREZID",…
Answer: limma-voom: Calculate the log-fold change in gene expression within a sample
by
Gordon Smyth
50k
No, you cannot use residuals to compute logFCs. From the information you give, I guess that you need to add individual-specific condition …
Comment: Error EPICv2 ChAMP
by
James W. MacDonald
65k
You don't need to do either of the above suggestions. ``` library(BiocManager) install("YuanTian1991/ChAMPdata") ``` will install without…
Votes
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
Answer: Differentially expressed genes in monocle pseudotime
Answer: DESeq2 - dispersion estimation when there is none
Awards
• All
Scholar
to
Gordon Smyth
50k
Popular Question
to
taur.vil
• 0
Teacher
to
Yuan Tian
▴ 280
Popular Question
to
Charlotte Soneson
▴ 170
Popular Question
to
mpuli011
• 0
Locations
• All
Germany,
just now
United States,
1 minute ago
France,
9 minutes ago
China,
27 minutes ago
France,
49 minutes ago
Traffic: 479 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