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CGH
•
reset
0
votes
9
replies
1.7k
views
gains and losses via mode shifting
Cancer
CGH
Cancer
CGH
15.8 years ago
Oscar Rueda
▴ 60
0
votes
8
replies
2.0k
views
segmentation aCGH data
Normalization
CGH
probe
limma
DNAcopy
snapCGH
Normalization
CGH
probe
limma
DNAcopy
16.6 years ago
jhs1jjm@leeds.ac.uk
▴ 230
0
votes
8
replies
1.6k
views
annotation files for agilent: a bit off-topic
Annotation
CGH
Annotation
CGH
updated 16.8 years ago by
Gaj Stan BIGCAT
▴ 100 • written 16.8 years ago by
Weiwei Shi
★ 1.2k
0
votes
7
replies
1.8k
views
segmentation for Affy SNP arrays
SNP
CGH
affy
GLAD
snapCGH
SNP
CGH
affy
GLAD
snapCGH
updated 16.6 years ago by
Rob Scharpf
▴ 250 • written 16.6 years ago by
Yu Chuan Tai
▴ 440
0
votes
7
replies
1.6k
views
processCGH in snapCGH package
CGH
snapCGH
CGH
snapCGH
updated 16.6 years ago by
Sean Davis
21k • written 16.6 years ago by
jhs1jjm@leeds.ac.uk
▴ 230
0
votes
7
replies
1.4k
views
CGH analysis without genome positions
CGH
CGH
updated 14.1 years ago by
Sean Davis
21k • written 14.1 years ago by
adam_pgsql
▴ 70
0
votes
5
replies
1.6k
views
from BAC name to list of genes in that BAC
CGH
BAC
CGH
BAC
updated 17.3 years ago by
Hilmar Berger
▴ 60 • written 17.3 years ago by
Federico Abascal
▴ 90
0
votes
5
replies
1.2k
views
quality assessment and preprocessing for tiling array-based CGH data
CGH
probe
CGH
probe
updated 15.5 years ago by
Sean Davis
21k • written 15.5 years ago by
Leon Yee
▴ 110
0
votes
5
replies
1.2k
views
gains and losses via mode shifting
CGH
CGH
updated 15.9 years ago by
Sean Davis
21k • written 15.9 years ago by
Benjamin Otto
▴ 830
0
votes
5
replies
1.6k
views
understanding GOstats p-value
Annotation
GO
Cancer
CGH
GOstats
Annotation
GO
Cancer
CGH
GOstats
updated 16.3 years ago by
Charles Berry
▴ 290 • written 16.3 years ago by
Janet Young
▴ 740
0
votes
4
replies
1.4k
views
running time of snapCGH processCGH and runDNAcopy
aCGH
Survival
CGH
annotate
genefilter
affy
DNAcopy
aCGH
GLAD
tilingArray
snapCGH
aCGH
updated 16.6 years ago by
jhs1jjm@leeds.ac.uk
▴ 230 • written 16.6 years ago by
caiwei@mdanderson.org
▴ 110
0
votes
4
replies
1.1k
views
create CNA object in DNAcopy package with agilent data
CGH
CGH
updated 16.6 years ago by
Sean Davis
21k • written 16.6 years ago by
jhs1jjm@leeds.ac.uk
▴ 230
0
votes
4
replies
1.3k
views
Agilent CGH data
CGH
arrayQuality
marray
CGH
arrayQuality
marray
updated 16.6 years ago by
Sean Davis
21k • written 16.6 years ago by
jhs1jjm@leeds.ac.uk
▴ 230
2
votes
3
replies
1.2k
views
read.maimages
Annotation
CGH
limma
Annotation
CGH
limma
updated 6.6 years ago by
Gordon Smyth
50k • written 11.8 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
1.0k
views
Scripts to handle array CGH data files from NimbleGen
aCGH
Cancer
Breast
CGH
aCGH
aCGH
Cancer
Breast
CGH
aCGH
updated 17.9 years ago by
Todd Richmond
▴ 140 • written 17.9 years ago by
Steven McKinney
▴ 310
5
votes
3
replies
1.6k
views
Classes and methods for working with segmented copy number data
cgh
copynumber
updated 7.1 years ago by
Marcel Ramos
690 • written 7.7 years ago by
Sean Davis
21k
0
votes
3
replies
1.2k
views
[JOB] Bioinformatics positions at NCI
SNP
Cancer
CGH
affy
SNP
Cancer
CGH
affy
updated 18.0 years ago by
E Motakis, Mathematics
▴ 190 • written 18.0 years ago by
Sean Davis
21k
0
votes
3
replies
2.5k
views
Script to save plots in Pdf format ( DNAcopy)
CGH
PROcess
CGH
PROcess
updated 13.1 years ago by
Thomas Hampton
▴ 750 • written 13.1 years ago by
nac
▴ 280
0
votes
2
replies
898
views
Fwd: Re: cross species CGH Nimblegene arrays
CGH
CGH
updated 16.0 years ago by
Sean Davis
21k • written 16.0 years ago by
mb23
▴ 30
0
votes
2
replies
1.2k
views
imputing missing data for 70mer array platform, need advice
aCGH
CGH
multtest
impute
aCGH
oligo
aCGH
CGH
multtest
impute
aCGH
oligo
updated 17.3 years ago by
Sean Davis
21k • written 17.3 years ago by
Betty Gilbert
▴ 50
0
votes
2
replies
855
views
Single channel CGH analysis [was Re: Bioconductor Digest, Vol 62, Issue 3]
CGH
CGH
updated 16.1 years ago by
Abhilash Venu
▴ 340 • written 16.1 years ago by
Sean Davis
21k
0
votes
2
replies
1.1k
views
cross species CGH Nimblegene arrays
CGH
CGH
updated 16.0 years ago by
Alicia Oshlack
▴ 70 • written 16.0 years ago by
mb23
▴ 30
0
votes
2
replies
1.1k
views
How to display chromosome rapresentation ?
CGH
impute
CGH
impute
updated 15.1 years ago by
Sean Davis
21k • written 15.1 years ago by
Giulio Di Giovanni
▴ 540
0
votes
2
replies
1.3k
views
Calling genes present or absent in CGH data
CGH
limma
CGH
limma
updated 14.3 years ago by
Sean Davis
21k • written 14.3 years ago by
adam_pgsql
▴ 70
0
votes
2
replies
1.5k
views
Nimblegen CGH ringo to snapCGH
CGH
snapCGH
Ringo
CGH
snapCGH
Ringo
updated 14.0 years ago by
Joern Toedling
▴ 450 • written 14.0 years ago by
Chris Fenton
▴ 80
0
votes
2
replies
1.2k
views
memory limit
CGH
trigger
CGH
trigger
updated 13.6 years ago by
Steve Lianoglou
★ 13k • written 13.6 years ago by
Noemi Andor
▴ 100
1
vote
2
replies
2.4k
views
Columns used by read.maimages for Agilent arrays
Annotation
CGH
limma
11.8 years ago • updated 6.6 years ago
Gordon Smyth
50k
0
votes
1
reply
1.1k
views
Agilent Human Genome CGH 44K annotation
Annotation
Cancer
CGH
Annotation
Cancer
CGH
updated 15.7 years ago by
Sean Davis
21k • written 15.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
975
views
normexp error (while using snapCGH)
CGH
snapCGH
CGH
snapCGH
updated 15.6 years ago by
Artur Veloso
▴ 340 • written 15.6 years ago by
Abhilash Venu
▴ 340
0
votes
1
reply
1.5k
views
Question regarding the use of the snapCGH package to analyze aCGH data obtained from TCGA
Microarray
Annotation
CGH
snapCGH
Microarray
Annotation
CGH
snapCGH
updated 9.7 years ago by
Sean Davis
21k • written 9.7 years ago by
Guest User
★ 13k
0
votes
1
reply
1.5k
views
CNV analysis with cghMCR/CNTools
GO
CGH
hgu133a
hgu95av2
GO
CGH
hgu133a
hgu95av2
updated 14.3 years ago by
John Zhang
★ 2.9k • written 14.3 years ago by
Tim Smith
★ 1.1k
0
votes
1
reply
991
views
Scripts to handle array CGH data files from NimbleGen
CGH
tilingArray
CGH
tilingArray
updated 17.7 years ago by
ma3mls@bath.ac.uk
▴ 40 • written 17.7 years ago by
Todd Richmond
▴ 140
0
votes
1
reply
1.2k
views
How to use snapCGH with Nimblegen data
CGH
snapCGH
CGH
snapCGH
updated 17.6 years ago by
Steven McKinney
▴ 310 • written 17.6 years ago by
rdesprat
▴ 30
0
votes
1
reply
735
views
CGH analysis in non-model organism
CGH
CGH
updated 15.4 years ago by
Sean Davis
21k • written 15.4 years ago by
Mingkwan Nipitwattanaphon
▴ 30
0
votes
1
reply
1.3k
views
limma Agilent Normalization
Normalization
CGH
Normalization
CGH
updated 13.9 years ago by
Sean Davis
21k • written 13.9 years ago by
Noemi Andor
▴ 100
0
votes
1
reply
1.4k
views
aCGH...'Genomic events'
CGH
CGH
updated 13.7 years ago by
Sean Davis
21k • written 13.7 years ago by
BTIS Department
▴ 10
0
votes
1
reply
987
views
Where to download annotation package for Agilent human CGH 44B
Annotation
CGH
Annotation
CGH
updated 15.2 years ago by
Marc Carlson
★ 7.2k • written 15.2 years ago by
Daren Tan
▴ 190
0
votes
1
reply
1.6k
views
how to import Agilent CGH custom design xml file into limma
aCGH
CGH
probe
aCGH
snapCGH
aCGH
CGH
probe
aCGH
snapCGH
updated 13.5 years ago by
Sean Davis
21k • written 13.5 years ago by
Jarek Bryk
▴ 110
0
votes
1
reply
1.3k
views
A CGH platform question
SNP
Genetics
Coverage
CGH
affy
SNP
Genetics
Coverage
CGH
affy
updated 15.4 years ago by
Henrik Bengtsson
★ 2.4k • written 15.4 years ago by
Johan Lindberg
▴ 70
0
votes
1
reply
1.3k
views
Bioconductor 2.1 is released
SNP
Microarray
SAGE
Annotation
Bayesian
Regression
GUI
CGH
hgu95av2
graph
Rgraphviz
SNP
16.6 years ago
Hervé Pagès
16k
0
votes
1
reply
795
views
error message from GLAD
CGH
GLAD
CGH
GLAD
updated 18.7 years ago by
Philippe Hupé
▴ 20 • written 18.7 years ago by
Irene Li
▴ 30
0
votes
1
reply
1.4k
views
CGHweb and cghFLasso
CGH
CGH
updated 12.6 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.6 years ago by
Chris Fenton
▴ 80
0
votes
1
reply
1.3k
views
CNTools error message
CGH
probe
DNAcopy
CGH
probe
DNAcopy
updated 12.3 years ago by
Martin Morgan
25k • written 12.3 years ago by
nac
▴ 280
0
votes
1
reply
1.4k
views
Bioconductor 1.4 released
Proteomics
Annotation
Normalization
GO
Cancer
CGH
pamr
gcrma
gpls
affyPLM
webbioc
bim
updated 20.0 years ago by
Wolfgang Huber
★ 13k • written 20.0 years ago by
A.J. Rossini
▴ 810
0
votes
1
reply
813
views
How to run bioHMM on Affymetrix data?
CGH
CGH
updated 15.1 years ago by
Oosting, J. PATH
▴ 550 • written 15.1 years ago by
Stacey Burrows
▴ 30
0
votes
1
reply
707
views
aCGH across samples
aCGH
Cancer
CGH
aCGH
aCGH
Cancer
CGH
aCGH
updated 17.4 years ago by
Sean Davis
21k • written 17.4 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
1.1k
views
DNAcopy package, craeting CNA object
CGH
marray
DNAcopy
CGH
marray
DNAcopy
updated 16.7 years ago by
Sean Davis
21k • written 16.7 years ago by
jhs1jjm@leeds.ac.uk
▴ 230
0
votes
1
reply
914
views
NimbleGen HG18 CGH data
aCGH
CGH
aCGH
aCGH
CGH
aCGH
updated 14.8 years ago by
Sean Davis
21k • written 14.8 years ago by
Abcis
▴ 10
0
votes
1
reply
1.1k
views
array CGH - raw data analysis
CGH
CGH
updated 16.2 years ago by
Sean Davis
21k • written 16.2 years ago by
João Fadista
▴ 500
0
votes
1
reply
1.3k
views
CGH analysis warning messages
Cancer
CGH
snapCGH
Cancer
CGH
snapCGH
updated 16.8 years ago by
Ian Roberts
▴ 70 • written 16.8 years ago by
Daniel Brewer
★ 1.9k
50 results • Page
1 of 1
Recent ...
Replies
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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