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makecdfenv
•
reset
2
votes
8
replies
4.0k
views
Clariom D Human Microarray CDF file to package
simpleaffy
makecdfenv
7.5 years ago
jayme.rickman
• 0
1
vote
4
replies
2.9k
views
Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
miRNA
Microarray
cdf
makecdfenv
miRNA
Microarray
cdf
makecdfenv
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Guest User
★ 13k
0
votes
2
replies
2.4k
views
Importing CDF file for custom array using makecdfenv
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 17.6 years ago by
Michal Okoniewski
▴ 120 • written 17.6 years ago by
Ann Hess
▴ 340
0
votes
0
replies
1.8k
views
Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
miRNA
Annotation
cdf
makecdfenv
miRNA
Annotation
cdf
makecdfenv
10.2 years ago
Isaac Neuhaus
▴ 360
0
votes
4
replies
1.7k
views
affyPLM and exon array question
cdf
affy
makecdfenv
affyPLM
cdf
affy
makecdfenv
affyPLM
updated 16.9 years ago by
Ben Bolstad
★ 1.2k • written 16.9 years ago by
Allen Day
▴ 30
0
votes
3
replies
1.7k
views
CDF package in R (windows)
cdf
affy
makecdfenv
cdf
affy
makecdfenv
16.8 years ago
Salim Charaniya
▴ 20
0
votes
3
replies
1.6k
views
unable to install GenomeWideSNP_6 cdf
makecdfenv
bioclite
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
vinaysbharadhwaj
• 0
0
votes
1
reply
1.6k
views
Reading MAGE-ML cdf into bioconductor for limma in R v. 3.0.2
Microarray
cdf
probe
makecdfenv
RMAGEML
ArrayExpress
Microarray
cdf
probe
makecdfenv
updated 10.0 years ago by
James W. MacDonald
65k • written 10.0 years ago by
Guest User
★ 13k
0
votes
9
replies
1.6k
views
gcrma error? - linked to makeProbePackage ?
cdf
probe
affy
makecdfenv
gcrma
matchprobes
cdf
probe
affy
makecdfenv
gcrma
matchprobes
updated 16.7 years ago by
James W. MacDonald
65k • written 16.7 years ago by
Benoit Ballester
▴ 90
0
votes
4
replies
1.5k
views
error with makecdfenv package
Annotation
cdf
makecdfenv
oligo
xps
Annotation
cdf
makecdfenv
oligo
xps
updated 9.7 years ago by
cstrato
★ 3.9k • written 9.7 years ago by
James W. MacDonald
65k
0
votes
5
replies
1.5k
views
Importing CDF file for custom array using makecdfenv
Microarray
GO
Survival
Cancer
cdf
Biobase
annotate
genefilter
affy
graph
makecdfenv
GO
updated 17.4 years ago by
Sung-Chur Sim
▴ 20 • written 17.4 years ago by
Jenny Drnevich
★ 2.2k
0
votes
2
replies
1.5k
views
RE:proper pooling design
Microarray
Normalization
affy
makecdfenv
limma
marray
Microarray
Normalization
affy
limma
updated 20.2 years ago by
YUK FAI LEUNG
▴ 140 • written 20.2 years ago by
Stephen Moore
▴ 70
0
votes
0
replies
1.5k
views
Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
miRNA
cdf
affy
makecdfenv
affxparser
miRNA
cdf
affy
makecdfenv
affxparser
10.2 years ago
James W. MacDonald
65k
2
votes
4
replies
1.5k
views
Help with microarray analysis (forming cdf files)
microarray
affy
makecdfenv
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
SSK
▴ 10
0
votes
5
replies
1.4k
views
Affymetrix Promoter tiling array
cdf
makecdfenv
cdf
makecdfenv
17.6 years ago
Wu, Xiwei
▴ 350
0
votes
3
replies
1.3k
views
Working flow_own CEL file reading problem
Normalization
cdf
affy
makecdfenv
Normalization
cdf
affy
makecdfenv
updated 18.8 years ago by
James W. MacDonald
65k • written 18.8 years ago by
Junshi Yazaki
▴ 40
0
votes
3
replies
1.3k
views
R crashes when using CDF package generated using makecdfenv
cdf
makecdfenv
cdf
makecdfenv
updated 11.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 11.1 years ago by
Guest User
★ 13k
0
votes
0
replies
1.3k
views
How to make a custom cdf file?
Annotation
cdf
probe
makecdfenv
Annotation
cdf
probe
makecdfenv
12.2 years ago
Olivier Lucas
▴ 40
0
votes
2
replies
1.3k
views
Creating Custom CDF
cdf
makecdfenv
cdf
makecdfenv
updated 14.7 years ago by
James W. MacDonald
65k • written 14.7 years ago by
naresh kumar
▴ 40
0
votes
1
reply
1.2k
views
Prokaryotic_Rhodobacter capsulatus GEP
Epigenetics
cdf
affy
makecdfenv
plier
affxparser
preprocessCore
Epigenetics
cdf
affy
updated 15.3 years ago by
dorothyc
▴ 140 • written 15.3 years ago by
James W. MacDonald
65k
0
votes
2
replies
1.2k
views
Using Affymetrix PM chips with Bioconductor
Annotation
cdf
probe
makecdfenv
Annotation
cdf
probe
makecdfenv
updated 15.0 years ago by
Ben Bolstad
★ 1.2k • written 15.0 years ago by
James Mcininch
▴ 20
0
votes
2
replies
1.2k
views
affy : ReadAffy() fails on HuGene-1_1-st-v1 chips
Microarray
cdf
affy
makecdfenv
PROcess
oligo
cycle
Microarray
cdf
affy
makecdfenv
oligo
updated 12.1 years ago by
James W. MacDonald
65k • written 12.1 years ago by
Groot, Philip de
▴ 630
0
votes
4
replies
1.2k
views
makecdfenv
cdf
makecdfenv
cdf
makecdfenv
updated 17.3 years ago by
Martin Morgan
25k • written 17.3 years ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
1.2k
views
Trouble in making the cdf package for Arabidopsis?
cdf
probe
makecdfenv
cdf
probe
makecdfenv
updated 21.1 years ago by
Rafael A. Irizarry
▴ 640 • written 21.1 years ago by
Hua Liu
▴ 20
0
votes
1
reply
1.1k
views
warning from make.cdf.package - FYI
GO
Survival
cdf
Biobase
annotate
genefilter
graph
makecdfenv
limma
gcrma
matchprobes
GO
updated 17.4 years ago by
James W. MacDonald
65k • written 17.4 years ago by
Jenny Drnevich
★ 2.2k
0
votes
6
replies
1.1k
views
mas5calls with make.cdf.env
cdf
probe
makecdfenv
cdf
probe
makecdfenv
updated 16.8 years ago by
James W. MacDonald
65k • written 16.8 years ago by
Lana Schaffer
★ 1.3k
0
votes
2
replies
1.1k
views
Error message (probably) from AffyBatch.R when using a modified CDF
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 11.2 years ago by
James W. MacDonald
65k • written 11.2 years ago by
Hugh Shanahan
▴ 50
0
votes
3
replies
1.1k
views
INstalling devel version
Microarray
Pharmacogenomics
Annotation
GO
Cancer
cdf
probe
affy
makecdfenv
limma
annaffy
19.6 years ago
Mayte Suarez-Farinas
▴ 300
0
votes
1
reply
1.1k
views
How to create a custom CDF ?
mgu74av2
cdf
probe
affy
makecdfenv
gcrma
mgu74av2
cdf
probe
affy
makecdfenv
gcrma
updated 19.7 years ago by
Ben Bolstad
★ 1.1k • written 19.7 years ago by
Alexander Stoddard
▴ 10
0
votes
5
replies
1.1k
views
makecdfenv and multi-mapping probes on Mouse Gene 1.0 ST array
cdf
probe
makecdfenv
cdf
probe
makecdfenv
updated 15.9 years ago by
Sean Davis
21k • written 15.9 years ago by
Heidi Dvinge
★ 2.0k
0
votes
0
replies
1.1k
views
[R] make.cdf.package: Error: cannot allocate vector of size 1 Kb
Cancer
cdf
affy
makecdfenv
Cancer
cdf
affy
makecdfenv
14.2 years ago
James W. MacDonald
65k
0
votes
1
reply
1.1k
views
solicitation for Affy bovine cdf environment
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 18.9 years ago by
James W. MacDonald
65k • written 18.9 years ago by
Anjanette Watson
▴ 10
0
votes
2
replies
1.1k
views
how to make probe environments for use with GCRMA
cdf
makecdfenv
gcrma
cdf
makecdfenv
gcrma
updated 16.7 years ago by
claire
▴ 50 • written 16.7 years ago by
Wittner, Ben
▴ 290
0
votes
2
replies
1.1k
views
Creating Affymetrix CDF files
cdf
probe
makecdfenv
convert
cdf
probe
makecdfenv
convert
updated 15.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 15.2 years ago by
Mehmet Somel
▴ 20
0
votes
1
reply
1.0k
views
making a cdf file for expression analysis on a tiling array
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 17.1 years ago by
Sean Davis
21k • written 17.1 years ago by
Ivan Baxter
▴ 60
0
votes
1
reply
1.0k
views
new user trying to create a cdf package for custom array
cdf
probe
affy
makecdfenv
cdf
probe
affy
makecdfenv
updated 17.6 years ago by
James W. MacDonald
65k • written 17.6 years ago by
Schwartz, Donald
▴ 20
0
votes
0
replies
1.0k
views
make CDF env (fwd)
Cancer
cdf
affy
makecdfenv
Cancer
cdf
affy
makecdfenv
21.0 years ago
Wolfgang Huber
★ 13k
0
votes
1
reply
1.0k
views
affymetrix CDF file problem
cdf
makecdfenv
cdf
makecdfenv
updated 18.8 years ago by
James W. MacDonald
65k • written 18.8 years ago by
Karin Lagesen
▴ 80
0
votes
2
replies
1.0k
views
Missing probesets
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 18.9 years ago by
rgentleman
★ 5.5k • written 18.9 years ago by
Malick.PAYE@eu.biomerieux.com
▴ 110
0
votes
2
replies
996
views
makecdfenv crashes
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 15.3 years ago by
James W. MacDonald
65k • written 15.3 years ago by
Skewes,Aaron
▴ 60
0
votes
1
reply
994
views
problem in make.cdf.package of MoGene-1_0-st-v1.r3.CDF
cdf
makecdfenv
cdf
makecdfenv
updated 14.5 years ago by
Benilton Carvalho
★ 4.3k • written 14.5 years ago by
Peng Yu
▴ 940
0
votes
2
replies
970
views
makecdfenv error
cdf
makecdfenv
cdf
makecdfenv
updated 18.9 years ago by
James W. MacDonald
65k • written 18.9 years ago by
Ambika Sundaresan
▴ 10
0
votes
1
reply
965
views
Small bug in function 'countskip.FASTA.entries' from package 'altcdfenvs'
probe
affy
makecdfenv
matchprobes
altcdfenvs
probe
affy
makecdfenv
matchprobes
altcdfenvs
updated 18.3 years ago by
lgautier@altern.org
▴ 950 • written 18.4 years ago by
Norman Pavelka
▴ 190
0
votes
2
replies
961
views
cdf environment for bovine Affy chips
cdf
makecdfenv
cdf
makecdfenv
19.1 years ago
Margaret Gardiner-Garden
▴ 160
0
votes
1
reply
947
views
affyPLM and exon array question
cdf
affy
makecdfenv
affyPLM
cdf
affy
makecdfenv
affyPLM
updated 16.5 years ago by
Ben Bolstad
★ 1.2k • written 16.5 years ago by
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
943
views
How do I install custom made CDF in Bioconductor
cdf
makecdfenv
cdf
makecdfenv
18.6 years ago
Ruppert Valentino
▴ 270
0
votes
0
replies
894
views
a question about getCdfInfo package in GCRMA, thanks for your help.
Annotation
cdf
makecdfenv
Annotation
cdf
makecdfenv
12.4 years ago
boczniak767
▴ 720
0
votes
0
replies
847
views
(no subject)
cdf
affy
makecdfenv
convert
cdf
affy
makecdfenv
convert
17.2 years ago
Charlyn Suarez
▴ 10
0
votes
1
reply
835
views
error in makecdfenv
makecdfenv
makecdfenv
updated 16.5 years ago by
James W. MacDonald
65k • written 16.5 years ago by
Yan Zhang
▴ 130
0
votes
1
reply
833
views
Fusarium CDF
cdf
makecdfenv
cdf
makecdfenv
updated 17.9 years ago by
James W. MacDonald
65k • written 17.9 years ago by
Heather Erika Hallen
▴ 30
50 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
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Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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