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
437
views
Obtaining pheno data from CEL files
GEO
affy
29 days ago • updated 22 days ago
Kurtis
• 0
1
vote
2
replies
227
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
5 weeks ago
Mj.A.
• 0
1
vote
3
replies
359
views
frma normalization
frmaTools
affy
updated 10 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
michelafrancesconi8
• 0
0
votes
1
reply
603
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
885
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 12 months ago by
Pratik Mehta
▴ 10
0
votes
3
replies
1.5k
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
6
replies
2.1k
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
3
votes
9
replies
2.3k
views
Installing 'affy' package on MacOS M2 chip
nlme
affy
preprocessCore
updated 18 months ago by
James W. MacDonald
65k • written 18 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
854
views
Reading Affymetrix Axiom files
affy
SNP
axiom
3.0 years ago
f.calboli
• 0
1
vote
3
replies
965
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
985
views
Subscript out of bounds while normalising using affy::rma()
Normalization
affy
AffymetrixChip
3.0 years ago
geoffrey
▴ 10
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
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
657
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
989
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 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Marco_aurelio
• 0
1
vote
1
reply
636
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
1.0k
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
927
views
Problem analyzing Affymetrix Microarray data from Clariom S Mouse
affy
oligo
Clariom S Mouse
microarray
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
lsbew
• 0
0
votes
1
reply
592
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
3.8k • 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 4.1 years ago by
James W. MacDonald
65k • written 4.1 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
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
0
votes
1
reply
864
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
3
votes
2
replies
875
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
931
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
985
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
2.4k
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
729
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
0
votes
0
replies
761
views
Fold Change Calculation in edge package
edge
microarray
limma
affy
4.9 years ago
soumyab.g
▴ 10
6
votes
8
replies
1.8k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma
microarray
affy
edger
4.9 years ago
Jurat Shahidin
▴ 80
1
vote
2
replies
773
views
"hgu133plus2db" package not working in R
microarray
affy
annotation
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
rgeysels
• 0
2
votes
8
replies
1.4k
views
affycoretools package, HTA 2.0 annotation query
annotation
affy
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
a.karanikolou
▴ 10
0
votes
0
replies
646
views
table (pData(eset_NONE)[,"Study"]); table(pData(eset_NONE)[,"Disease"]);
affy
insilicomerging
5.1 years ago
pratikshasharma47
• 0
0
votes
0
replies
730
views
How to color samples in boxplot based on treatment or control using covdesc file
affy
boxplot
5.1 years ago
pratikshasharma47
• 0
3
votes
5
replies
1.1k
views
HTA 2.0 Differential expression analysis - design question
limma
hta
affy
annotation
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
RV
▴ 10
0
votes
1
reply
698
views
Differentially expressed genes in rice affymetrix data and annotation
affy
microarray
differentially expresed genes
limma
annotation
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
pratikshasharma47
• 0
1
vote
1
reply
697
views
Microaaray data analysis
affy
updated 5.1 years ago by
James W. MacDonald
65k • written 5.1 years ago by
p20180416
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
Awards
• All
Scholar
to
Rory Stark
★ 5.2k
Popular Question
to
tangming2005
▴ 190
Popular Question
to
Ian D.
▴ 70
Popular Question
to
junhui.li11
• 0
Scholar
to
James W. MacDonald
65k
Locations
• All
Germany,
14 minutes ago
United States,
30 minutes ago
WEHI, Melbourne, Australia,
46 minutes ago
Cambridge, UK,
1 hour ago
Canada,
2 hours ago
Traffic: 528 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