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cdf
•
reset
0
votes
3
replies
1.4k
views
trouble using GCRMA
Yeast
cdf
gcrma
Yeast
cdf
gcrma
updated 18.4 years ago by
Zhijin Jean Wu
▴ 200 • written 18.4 years ago by
wong
▴ 10
0
votes
1
reply
1.1k
views
Affy Human Gene ST1.0 cdf
Annotation
cdf
Annotation
cdf
updated 18.4 years ago by
James W. MacDonald
68k • written 18.4 years ago by
rcaloger
▴ 500
0
votes
0
replies
1.1k
views
Fwd: limma gene symbol not avialable problem
Microarray
Annotation
Cancer
cdf
probe
annotate
affy
affydata
limma
matchprobes
affyio
18.4 years ago
lidaof
▴ 450
0
votes
3
replies
1.7k
views
limma gene symbol not avialable problem
cdf
affy
affydata
limma
affylmGUI
affyio
cdf
affy
affydata
limma
affylmGUI
affyio
updated 18.4 years ago by
James W. MacDonald
68k • written 18.4 years ago by
lidaof
▴ 450
0
votes
0
replies
1.2k
views
Normalization of 2 color Nimblegen array
cdf
affy
affyPLM
convert
oligo
makePlatformDesign
cdf
affy
affyPLM
convert
oligo
18.4 years ago
dhruv pant
▴ 30
0
votes
6
replies
1.5k
views
mas5calls with make.cdf.env
cdf
probe
makecdfenv
cdf
probe
makecdfenv
updated 18.4 years ago by
James W. MacDonald
68k • written 18.4 years ago by
Lana Schaffer
★ 1.3k
0
votes
3
replies
2.1k
views
CDF package in R (windows)
cdf
affy
makecdfenv
cdf
affy
makecdfenv
18.4 years ago
Salim Charaniya
▴ 20
0
votes
0
replies
1.0k
views
problem with hyperGTest function
GO
Cancer
cdf
GOstats
GO
Cancer
cdf
GOstats
18.4 years ago
Seth Falcon
★ 7.4k
0
votes
3
replies
1.4k
views
Affy normalization with custom chip.
cdf
affy
cdf
affy
updated 18.4 years ago by
Jenny Drnevich
★ 2.2k • written 18.4 years ago by
Daniel Gatti
▴ 70
0
votes
2
replies
755
views
QCReport problem
cdf
cdf
updated 18.4 years ago by
James W. MacDonald
68k • written 18.4 years ago by
Sanchita Bhattacharya
▴ 10
0
votes
9
replies
2.4k
views
problem with function rma
Normalization
rat2302
cdf
genefilter
affy
simpleaffy
affyQCReport
affyio
Normalization
updated 18.4 years ago by
Seth Falcon
★ 7.4k • written 18.4 years ago by
julin@aecom.yu.edu
▴ 80
0
votes
6
replies
1.9k
views
mas5 update.default problem
hgu95av2
cdf
affy
affyio
hgu95av2
cdf
affy
affyio
updated 18.4 years ago by
Seth Falcon
★ 7.4k • written 18.4 years ago by
David Ruau
▴ 190
0
votes
0
replies
821
views
(no subject)
hgu95av2
cdf
affy
affyio
hgu95av2
cdf
affy
affyio
18.4 years ago
David Ruau
▴ 190
0
votes
0
replies
1.1k
views
simpleaffy problem - drosophila2
drosophila2
cdf
affy
affydata
simpleaffy
drosophila2
cdf
affy
affydata
simpleaffy
18.5 years ago
Yihuan Xu
▴ 130
0
votes
9
replies
2.5k
views
problem with duplicateCorrelation and ExpressionSet objects
GO
Survival
cdf
Biobase
graph
limma
gcrma
annaffy
affyPLM
simpleaffy
biomaRt
Category
updated 18.5 years ago by
Seth Falcon
★ 7.4k • written 18.5 years ago by
Jenny Drnevich
★ 2.2k
0
votes
1
reply
1.2k
views
simpleaffy plot error
Survival
cdf
genefilter
simpleaffy
Survival
cdf
genefilter
simpleaffy
updated 18.5 years ago by
Crispin Miller
★ 1.1k • written 18.5 years ago by
Georg Otto
▴ 510
0
votes
1
reply
929
views
RMA warning message about missing se.exprs
Survival
Cancer
cdf
genefilter
simpleaffy
Survival
Cancer
cdf
genefilter
simpleaffy
updated 18.5 years ago by
Martin Morgan
25k • written 18.5 years ago by
caiwei@mdanderson.org
▴ 110
0
votes
2
replies
1.2k
views
Nimblegen data analysis
GO
cdf
affy
oligo
GO
cdf
affy
oligo
updated 18.5 years ago by
Todd Richmond
▴ 140 • written 18.5 years ago by
Jenny Drnevich
★ 2.2k
0
votes
4
replies
2.3k
views
affyPLM and exon array question
cdf
affy
makecdfenv
affyPLM
cdf
affy
makecdfenv
affyPLM
updated 18.5 years ago by
Ben Bolstad
★ 1.2k • written 18.5 years ago by
Allen Day
▴ 30
0
votes
1
reply
1.4k
views
paired design, LIMMA
cdf
tkWidgets
affy
widgetTools
limma
affyio
cdf
tkWidgets
affy
widgetTools
limma
affyio
updated 18.5 years ago by
Lev Soinov
▴ 470 • written 18.5 years ago by
Gordon Smyth
53k
0
votes
1
reply
1.2k
views
RMA error on exon arrays
Normalization
Breast
cdf
probe
PROcess
Normalization
Breast
cdf
probe
PROcess
updated 18.6 years ago by
James W. MacDonald
68k • written 18.6 years ago by
raffaele calogero
▴ 500
0
votes
1
reply
767
views
error getting CDF
cdf
gcrma
cdf
gcrma
updated 18.6 years ago by
James W. MacDonald
68k • written 18.6 years ago by
Yi Xing
▴ 20
0
votes
5
replies
1.5k
views
CDF/Probe/Annotation for GNF1m custom chip
cdf
probe
affylmGUI
cdf
probe
affylmGUI
updated 18.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 18.6 years ago by
Cei Abreu-Goodger
▴ 830
0
votes
3
replies
964
views
Affymetrix Tiling arrays
cdf
cdf
18.6 years ago
Alessandro Ferrantini
▴ 30
0
votes
0
replies
1.3k
views
affy u133x3p chip
Microarray
Genetics
GO
Preprocessing
Cancer
CGH
cdf
probe
annotate
genefilter
affy
RBGL
18.6 years ago
Dick Beyer
★ 1.4k
0
votes
0
replies
621
views
ANN:xy2i and i2xy to be deprecated
Microarray
Cancer
cdf
affy
Microarray
Cancer
cdf
affy
18.6 years ago
James W. MacDonald
68k
0
votes
1
reply
783
views
combineAffyBatch problem
cdf
affy
cdf
affy
updated 18.7 years ago by
Wolfgang Huber
★ 13k • written 18.7 years ago by
Gabor Halasz
▴ 10
0
votes
1
reply
1.1k
views
weird problem with ReadAffy and makecdfenv'd CDF package
cdf
cdf
updated 18.7 years ago by
James W. MacDonald
68k • written 18.7 years ago by
Tim
▴ 160
0
votes
4
replies
1.6k
views
metadata for Affymetrix Poplar array
Annotation
cdf
Annotation
cdf
updated 18.7 years ago by
Nianhua Li
▴ 870 • written 18.7 years ago by
Dick Beyer
★ 1.4k
0
votes
3
replies
1.7k
views
webbioc chicken
Microarray
cdf
probe
multtest
affy
webbioc
Microarray
cdf
probe
multtest
affy
webbioc
updated 18.7 years ago by
Nianhua Li
▴ 870 • written 18.7 years ago by
jane janes
▴ 20
0
votes
1
reply
1.4k
views
making a cdf file for expression analysis on a tiling array
cdf
affy
makecdfenv
cdf
affy
makecdfenv
updated 18.7 years ago by
Sean Davis
21k • written 18.7 years ago by
Ivan Baxter
▴ 60
0
votes
3
replies
1.4k
views
AffyQCReport: "I'm sorry, I do not know about chip type" (celeganscdf)
cdf
genefilter
affy
simpleaffy
affyQCReport
cdf
genefilter
affy
simpleaffy
affyQCReport
updated 18.7 years ago by
Crispin Miller
★ 1.1k • written 18.7 years ago by
Emmanuel Levy
▴ 270
0
votes
0
replies
1.2k
views
AffyQCReport: "I'm sorry, I do not know about chip type" (celeganscdf)
cdf
probe
genefilter
affy
simpleaffy
affyQCReport
cdf
probe
genefilter
affy
simpleaffy
18.7 years ago
Wu, Xiwei
▴ 350
0
votes
1
reply
1.4k
views
Problem with limma2biomaRt and MBNI custom CDF
Annotation
GO
cdf
DynDoc
genefilter
tkWidgets
affy
graph
limma
RBGL
biomaRt
Category
updated 18.7 years ago by
James W. MacDonald
68k • written 18.7 years ago by
Scott Ochsner
▴ 300
0
votes
4
replies
1.8k
views
error with AffyQCReport
cdf
annotate
affy
limma
RBGL
simpleaffy
GOstats
affyQCReport
cdf
annotate
affy
limma
updated 18.7 years ago by
Wolfgang Huber
★ 13k • written 18.7 years ago by
Mark W Kimpel
▴ 830
0
votes
0
replies
1.2k
views
Analysis with MBNI re-mapped (custom) CDF files
Microarray
Clustering
cdf
probe
affy
affyPLM
mmgmos
Microarray
Clustering
cdf
probe
18.8 years ago
Richard Pearson
▴ 390
0
votes
1
reply
1.5k
views
annaffy errors
GO
Survival
mgu74av2
cdf
annotate
affy
limma
gcrma
matchprobes
annaffy
simpleaffy
plier
updated 18.8 years ago by
James W. MacDonald
68k • written 18.8 years ago by
Ido M. Tamir
▴ 320
0
votes
0
replies
890
views
Bioconductor Digest, Vol 47, Issue 26
GO
cdf
probe
affy
gcrma
PROcess
convert
GO
cdf
probe
affy
gcrma
PROcess
convert
18.8 years ago
Manhong Dai
▴ 200
0
votes
2
replies
1.1k
views
Loading multiple Affy chips simultaneously
GO
cdf
gcrma
GO
cdf
gcrma
18.8 years ago
Paul Boutros
▴ 340
0
votes
4
replies
1.9k
views
Problems with the size of the plots obtained with AffyPLM
cdf
affy
gcrma
affyPLM
affyio
cdf
affy
gcrma
affyPLM
affyio
updated 18.8 years ago by
Oosting, J. PATH
▴ 550 • written 18.8 years ago by
Jordi Altirriba Gutiérrez
▴ 350
0
votes
0
replies
830
views
[Bioc] Removing outlier/masked probes and gcRMA
cdf
affy
gcrma
cdf
affy
gcrma
18.8 years ago
Amy Mikhail
▴ 460
0
votes
1
reply
904
views
Arabidopsis tiling arrays
cdf
cdf
updated 18.8 years ago by
Benilton Carvalho
★ 4.3k • written 18.8 years ago by
Liam Childs
▴ 10
0
votes
4
replies
1.6k
views
gcrma with bpmap file instead of cdf file
cdf
gcrma
cdf
gcrma
18.8 years ago
Baoqiang Cao
▴ 30
0
votes
2
replies
1.6k
views
simpleaffy and yeast2cdf problems
Survival
cdf
genefilter
affy
simpleaffy
Survival
cdf
genefilter
affy
simpleaffy
updated 18.8 years ago by
Alvord, Greg DMS [Contr]
▴ 160 • written 18.8 years ago by
Dan Swan
▴ 50
0
votes
0
replies
1.0k
views
Modified qc.affy code for chip type: soybeancdf
Cancer
cdf
Cancer
cdf
18.8 years ago
Alvord, Greg DMS [Contr]
▴ 160
0
votes
0
replies
1.1k
views
(no subject)
cdf
affy
makecdfenv
convert
cdf
affy
makecdfenv
convert
18.9 years ago
Charlyn Suarez
▴ 10
0
votes
2
replies
1.9k
views
problem with hist.default in affystart in package affycoretools
GO
cdf
annotate
affy
limma
RBGL
simpleaffy
GOstats
Category
affyQCReport
affyio
GO
cdf
updated 18.9 years ago by
James W. MacDonald
68k • written 18.9 years ago by
Kimpel, Mark W
▴ 890
0
votes
3
replies
1.9k
views
ExpressionSet, fitPLM confusion
cdf
probe
gcrma
matchprobes
affyPLM
affyio
cdf
probe
gcrma
matchprobes
affyPLM
affyio
updated 18.9 years ago by
Wolfgang Huber
★ 13k • written 18.9 years ago by
Georg Otto
▴ 510
0
votes
4
replies
1.5k
views
makecdfenv
cdf
makecdfenv
cdf
makecdfenv
updated 18.9 years ago by
Martin Morgan
25k • written 18.9 years ago by
Wolfgang Huber
★ 13k
0
votes
4
replies
1.3k
views
GCRMA with HG-U95A and HG-U95Av2
Normalization
cdf
gcrma
Normalization
cdf
gcrma
updated 18.9 years ago by
Seth Falcon
★ 7.4k • written 18.9 years ago by
Nicolas STRANSKY
▴ 10
927 results • Page
11 of 19
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Replies
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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