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 :
affy
•
reset
1
vote
10
replies
468
views
Obtaining pheno data from CEL files
GEO
affy
5 weeks ago • updated 4 weeks ago
Kurtis
• 0
1
vote
2
replies
233
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
6 weeks ago
Mj.A.
• 0
0
votes
6
replies
1.3k
views
LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?
affy
affy
updated 9 weeks ago by
Gordon Smyth
50k • written 19.0 years ago by
SAURIN
★ 1.1k
1
vote
3
replies
367
views
frma normalization
frmaTools
affy
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
michelafrancesconi8
• 0
0
votes
11
replies
2.1k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.7 years ago by
mike Ad.
▴ 30
0
votes
5
replies
2.0k
views
Normalizing Affy Almac Xcel Array Data from CEL files
Annotation
affy
oligo
ffpe
Annotation
affy
oligo
ffpe
written 10.3 years ago by
Guest User
★ 13k
0
votes
6
replies
2.2k
views
Error when Installing BioConductor Package ('affy')
Bioconductor
Install
affy
updated 5 months ago by
ATpoint
★ 4.1k • written 17 months ago by
laujihen
• 0
0
votes
2
replies
1.4k
views
Minimum expression threshold?
multtest
affy
multtest
affy
updated 8 months ago by
Amruta
• 0 • written 20.7 years ago by
Bob
▴ 20
0
votes
1
reply
621
views
affy package and SNP arrays
crlmm
hapmapsnp6
genomewidesnp6Crlmm
affy
updated 10 months ago by
Kevin Blighe
★ 3.9k • written 10 months ago by
Vincent J. Carey, Jr.
6.7k
2
votes
3
replies
905
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma
CustomCDF
Affyhgu133aExpr
limma
affy
updated 12 months ago by
James W. MacDonald
65k • written 13 months ago by
Pratik Mehta
▴ 10
0
votes
3
replies
1.6k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools
FRMA
affyio
AffymetrixDataTestFiles
affy
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Seymoo
• 0
0
votes
1
reply
1.3k
views
limma: decideTests
affy
limma
affy
limma
updated 15 months ago by
Gordon Smyth
50k • written 16.4 years ago by
Al Ivens
▴ 270
0
votes
0
replies
1.6k
views
limma: decideTests
limma
probe
affy
16.4 years ago • updated 15 months ago
Gordon Smyth
50k
3
votes
9
replies
2.3k
views
Installing 'affy' package on MacOS M2 chip
nlme
affy
preprocessCore
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
albrecht5698
• 0
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
RMP87
• 0
0
votes
0
replies
861
views
Reading Affymetrix Axiom files
affy
SNP
axiom
3.0 years ago
f.calboli
• 0
1
vote
3
replies
970
views
The eBayes function gives two p-values for each row
hgu133plus2.db
limma
DifferentialExpression
affy
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Caamp
• 0
2
votes
2
replies
989
views
Subscript out of bounds while normalising using affy::rma()
Normalization
affy
AffymetrixChip
3.0 years ago
geoffrey
▴ 10
0
votes
1
reply
1.4k
views
filtering on variance
probe
affy
probe
affy
updated 3.0 years ago by
Gordon Smyth
50k • written 16.4 years ago by
Dennis.Burian@faa.gov
▴ 90
0
votes
3
replies
3.7k
views
How do I choose between using affy or oligo package for preprocessing microarrays?
microarray
affymetrix microarrays
affy
oligo
updated 3.2 years ago by
James W. MacDonald
65k • written 7.3 years ago by
stevessheridan
• 0
0
votes
1
reply
2.0k
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
Lara
• 0
1
vote
2
replies
1.1k
views
Getting error in collapsing the affy probs
affy
eset
updated 3.3 years ago by
James W. MacDonald
65k • written 3.3 years ago by
AZ
▴ 30
0
votes
3
replies
1.4k
views
ReadAffy does not take into account parameter sampleNames with phenoData object
affycoretools
ReadAffy
Biobase
phenoData
affy
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
bastien_chassagnol
• 0
5
votes
8
replies
2.5k
views
how to annotate arrays
affy
annotation
microarray
oligo
updated 3.4 years ago by
James W. MacDonald
65k • written 8.8 years ago by
ben_cossins
• 0
1
vote
3
replies
2.4k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray
annotation
affy
3.6 years ago
kiera.lee
▴ 10
4
votes
7
replies
1.5k
views
Limma sample groups
microarray
limma
affy
cancer
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
nancy.nassar1590
• 0
0
votes
0
replies
667
views
Probe Design questions
probe
affy
3.6 years ago
henry1995910343
• 0
0
votes
2
replies
1.1k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0
microarray
affy
r
3.6 years ago
Marco_aurelio
• 0
0
votes
6
replies
1.1k
views
Problems loading latest Version of S4Vectors
affy
3.7 years ago
ianrector97
• 0
5
votes
9
replies
3.1k
views
Pipeline to analyzing Microarray data set( GSE files from NCBI GEO)
microarray
affy
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
adR
▴ 30
0
votes
2
replies
996
views
How to process triplicate cel data?
microarray
affy
cel
drugmatrix
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
peirinl
• 0
6
votes
3
replies
1.4k
views
GEOquery: preprocessing log of imported data
GEOquery
microarray
lumi
affy
limma
updated 3.9 years ago by
Sean Davis
21k • written 3.9 years ago by
fabian
▴ 40
2
votes
7
replies
1.2k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Marco_aurelio
• 0
1
vote
1
reply
648
views
Microarray Workflow - NA error
limma
affy
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
ammasakshay
• 0
3
votes
4
replies
1.1k
views
gcrma problem with make.cdf.package
gcrma
make.cdf.package
affy
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Osvaldo
▴ 40
0
votes
1
reply
934
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy
oligo
Clariom S Mouse
microarray
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
lsbew
• 0
0
votes
1
reply
602
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma
R
microarray
timepoint
affy
updated 4.1 years ago by
shepherl
3.9k • written 4.1 years ago by
ashwinmenon1994
• 0
1
vote
1
reply
1.0k
views
Trouble using affy library
software error
R
microarray
affy
updated 4.2 years ago by
James W. MacDonald
65k • written 4.2 years ago by
adam_casas
• 0
1
vote
1
reply
1.7k
views
How to annotate the Affymetrix data HTA-2.0 with oligo
annotation
affy
normalization
updated 4.2 years ago by
Guido Hooiveld
★ 3.9k • written 4.2 years ago by
sheikhbeigali
• 0
0
votes
2
replies
1.3k
views
3' microarray data using Affy - can't find cdf file, please help!
Affy
microarray
cdf
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
meganlloyd
• 0
0
votes
1
reply
873
views
limma Multi-level Experiments - Main effect test
limma
microarray
affy
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
cyusufd
• 0
0
votes
2
replies
1.0k
views
Ask for help on the preprocessing of GEO microarray data with Oligo and affy package
affy
rma
frma
oligo
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
chziy429
• 0
3
votes
2
replies
878
views
issue with hgu95acdf package
affy
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
alisher.jannyyev
• 0
0
votes
1
reply
942
views
Still Not Recognizing CDF
affy
CDF
4.5 years ago
ekl
• 0
1
vote
5
replies
1.7k
views
CDf files in R
affy
CDF
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
ekl
• 0
1
vote
2
replies
994
views
What should I do with the package:org.Hs.eg.db?
microarray
affy
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
2426986765
▴ 10
2
votes
4
replies
1.5k
views
Using function select
Affy
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
ekl
• 0
3
votes
8
replies
2.5k
views
Error: 'exprs<-' is not an exported object from 'namespace:affy'
affy
limma
piano
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
abolfazl.nikakhtar
• 0
0
votes
0
replies
733
views
Different versions of r/affy combination may lead to differences in rma normalization results
microarray
affy
rma normalization
affy package
4.7 years ago
yshuang
• 0
1
vote
2
replies
2.0k
views
CDF not found
Affy
microarray
updated 4.7 years ago by
Guido Hooiveld
★ 3.9k • written 4.7 years ago by
ijvechetti
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
Awards
• All
Popular Question
to
neilzhao
▴ 30
Popular Question
to
ATpoint
★ 4.1k
Teacher
to
Michael Love
42k
Popular Question
to
Haibo Liu
• 0
Popular Question
to
HS
▴ 10
Locations
• All
Germany,
1 minute ago
Egypt,
8 minutes ago
India,
11 minutes ago
United States,
20 minutes ago
The city by the bay,
41 minutes ago
Traffic: 524 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