Showing : affyio • reset
0
votes
9
replies
1.8k
views
problem with function rma
Normalization rat2302 cdf genefilter affy simpleaffy affyQCReport affyio Normalization
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 80
0
votes
8
replies
1.6k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 17.2 years ago by ★ 7.4k • written 17.2 years ago by ★ 2.2k
0
votes
6
replies
1.4k
views
mas5 update.default problem
hgu95av2 cdf affy affyio hgu95av2 cdf affy affyio
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 190
0
votes
5
replies
1.9k
views
affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 16.8 years ago by 65k • written 16.8 years ago by ▴ 50
0
votes
3
replies
997
views
beadarray example data problem 2
Biobase affy affyio beadarray Biobase affy affyio beadarray
17.5 years ago Martin Morgan 25k
0
votes
6
replies
1.9k
views
ReadAffy Error: new versions causing problems?
genefilter gcrma matchprobes simpleaffy affyio genefilter gcrma matchprobes simpleaffy
updated 16.9 years ago by ▴ 20 • written 17.0 years ago by ▴ 200
0
votes
5
replies
1.8k
views
RMA and justRMA error
Cancer cdf Biobase affy gcrma affyio Cancer cdf Biobase affy gcrma affyio
17.7 years ago Aedin Culhane ▴ 510
0
votes
4
replies
1.9k
views
Failure to load Biobase
Biobase affy limma gcrma matchprobes affyio Biobase affy limma gcrma matchprobes affyio
updated 18.0 years ago by 25k • written 18.0 years ago by ★ 2.2k
0
votes
3
replies
1.6k
views
beadarray package: problem with bead level data
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 16.8 years ago by ▴ 40 • written 16.8 years ago by ▴ 270
0
votes
3
replies
999
views
summarizing probe intensites before or after normalization- 1. how to do with RMA 2. Opinions?
Normalization probe affy affyio Normalization probe affy affyio
updated 17.7 years ago by ★ 1.2k • written 17.7 years ago by ▴ 420
0
votes
2
replies
1.3k
views
problem with latest version of graph
GO annotate genefilter multtest affy graph Rgraphviz RBGL GOstats affyio affycoretools
17.9 years ago Kimpel, Mark W ▴ 890
0
votes
7
replies
1.6k
views
Problems with affycomp - quantile.default
cdf affy affycomp affyio cdf affy affycomp affyio
updated 16.7 years ago by 65k • written 16.7 years ago by ▴ 380
0
votes
2
replies
2.9k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ▴ 360
0
votes
2
replies
1.3k
views
Changing the value of sampleNames for exprSet
affy affyio affy affyio
updated 17.7 years ago by 25k • written 17.7 years ago by ▴ 110
0
votes
2
replies
956
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio
updated 17.6 years ago by ★ 6.5k • written 17.6 years ago by ▴ 420
0
votes
3
replies
1.4k
views
pd.mapping 10Karray
BiocViews cdf affyio biocViews oligo pdInfoBuilder BufferedMatrix BiocViews BiocViews cdf
updated 16.7 years ago by ★ 7.4k • written 16.7 years ago by ▴ 10
0
votes
2
replies
1.6k
views
can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?
GO Survival Biobase genefilter affy limma RBGL GOstats Category affyio affycoretools GO
17.2 years ago Mark W Kimpel ▴ 830
0
votes
2
replies
1.0k
views
beadarray example data problem
Biobase affy affyio beadarray Biobase affy affyio beadarray
17.5 years ago Keith Satterley ▴ 450
0
votes
4
replies
1.4k
views
Quality control;Missing value;installation
Cancer cdf affy affyQCReport affyio arrayQualityMetrics Cancer cdf affy affyQCReport
updated 15.7 years ago by ★ 5.5k • written 15.7 years ago by ▴ 200
0
votes
2
replies
1.7k
views
cannot allocate vector of size 762 Mo ! One more time !
affy affyio trigger affy affyio trigger
updated 16.0 years ago by ★ 3.9k • written 16.0 years ago by ▴ 10
0
votes
3
replies
1.5k
views
*** caught segfault *** , cause 'memory not mapped'
affycoretools FRMA affyio AffymetrixDataTestFiles affy
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
2
replies
1.1k
views
vsm2
Survival geneplotter affy vsn limma affyio Survival geneplotter affy vsn limma affyio
updated 16.6 years ago by ★ 13k • written 16.6 years ago by ▴ 70
0
votes
3
replies
1.3k
views
limma gene symbol not avialable problem
cdf affy affydata limma affylmGUI affyio cdf affy affydata limma affylmGUI affyio
updated 16.9 years ago by 65k • written 16.9 years ago by ▴ 450
0
votes
3
replies
1.3k
views
GDS2eSet problems
Biobase affy convert affyio GEOquery Biobase affy convert affyio GEOquery
16.7 years ago Mcmahon, Wyatt ▴ 50
0
votes
4
replies
1.6k
views
Help with Affy TilingArray makePDpackage
affyio oligo affyio oligo
updated 16.2 years ago by ★ 1.2k • written 16.2 years ago by ▴ 40
0
votes
3
replies
1.6k
views
Tiling arrays and their probes
cdf affyio cdf affyio
updated 16.0 years ago by ★ 13k • written 16.0 years ago by ★ 13k
0
votes
4
replies
3.1k
views
Problems installing bioconductor on ubuntu
affyio affyio
updated 15.8 years ago by ★ 13k • written 15.8 years ago by ▴ 20
0
votes
1
reply
1.7k
views
gcrma background correction-saving output
cdf affy gcrma matchprobes affyio cdf affy gcrma matchprobes affyio
updated 5.3 years ago by 0 • written 17.4 years ago by ★ 2.2k
0
votes
1
reply
2.8k
views
ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 17.4 years ago by 65k • written 17.4 years ago by ▴ 510
0
votes
2
replies
1.5k
views
results of justPlier vs. RMA
Clustering affy plier affyio Clustering affy plier affyio
updated 17.5 years ago by ▴ 120 • written 17.5 years ago by ▴ 360
0
votes
1
reply
878
views
qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 17.7 years ago by 65k • written 17.7 years ago by ▴ 10
0
votes
1
reply
711
views
C entry point "ReadHeader" not in DLL for package "affy"
Biobase affy affyio Biobase affy affyio
updated 18.1 years ago by ★ 1.2k • written 18.1 years ago by ▴ 890
0
votes
2
replies
1.7k
views
summarizing probe intensites before or after normalization- 1. how to do with RMA 2. Opinions?
Microarray Normalization Preprocessing Cancer probe affy convert affyio Microarray Cancer
17.7 years ago James W. MacDonald 65k
0
votes
1
reply
1.3k
views
Problems with expresso
Preprocessing cdf affy affyio Preprocessing cdf affy affyio
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 380
0
votes
1
reply
1.1k
views
qc function missing in Linux version of simpleaffy
cdf genefilter affy affydata simpleaffy affyQCReport affyio cdf genefilter affy affydata
updated 17.8 years ago by 65k • written 17.8 years ago by ▴ 160
0
votes
1
reply
1.1k
views
An error of affylmGUI
cdf affy affylmGUI affyio cdf affy affylmGUI affyio
updated 16.7 years ago by ▴ 450 • written 16.7 years ago by ▴ 450
0
votes
1
reply
1.4k
views
ControlID Qcinfo slot in Illumina beadarray summary data?
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 16.7 years ago by ▴ 320 • written 16.7 years ago by ▴ 410
0
votes
1
reply
1.2k
views
beadarray readIllumina suggestions
Microarray Annotation geneplotter affy affyio beadarray quantsmooth beadarraySNP affy
updated 16.9 years ago by ▴ 460 • written 16.9 years ago by ▴ 10
0
votes
2
replies
948
views
steps to manually build AffyBatch object
GO affy affyio GO affy affyio
updated 17.1 years ago by 21k • written 17.1 years ago by ★ 1.2k
0
votes
1
reply
872
views
makePlatformDesign error
affyio oligo makePlatformDesign affyio oligo makePlatformDesign
updated 17.6 years ago by 65k • written 17.6 years ago by ▴ 20
0
votes
1
reply
964
views
Normalization in davidTiling demo
Normalization GO Survival genefilter geneplotter affy vsn tilingArray affyio GO Survival
updated 17.2 years ago by ★ 13k • written 17.2 years ago by ★ 1.3k
0
votes
2
replies
1.4k
views
problem updating packages OCPlus and RSNper
affy limma affyio OCplus affy limma affyio OCplus
updated 17.6 years ago by 16k • written 17.6 years ago by ▴ 890
0
votes
2
replies
1.1k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 17.6 years ago by ★ 1.2k • written 17.6 years ago by ▴ 420
0
votes
1
reply
1.1k
views
paired design, LIMMA
cdf tkWidgets affy widgetTools limma affyio cdf tkWidgets affy widgetTools limma affyio
updated 17.0 years ago by ▴ 470 • written 17.0 years ago by 50k
0
votes
2
replies
1.3k
views
Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1
affy gcrma matchprobes affyPLM affyio affy gcrma matchprobes affyPLM affyio
updated 17.9 years ago by ▴ 50 • written 17.9 years ago by ▴ 20
0
votes
2
replies
1.1k
views
median of the NUSE value
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 17.9 years ago by ★ 1.2k • written 17.9 years ago by ▴ 270
0
votes
2
replies
918
views
problem with CoCiteStats in bioC 1.8
cdf reposTools affy CoCiteStats affyio cdf reposTools affy CoCiteStats affyio
updated 18.0 years ago by ★ 7.4k • written 18.0 years ago by ▴ 890
0
votes
1
reply
1.5k
views
beadarray and BeadStudio v.2.3.41
Biobase affy affyio beadarray Biobase affy affyio beadarray
updated 17.2 years ago by ▴ 320 • written 17.3 years ago by ▴ 70
0
votes
1
reply
1.8k
views
using simpleaffy incorrectly, or is there a problem with the read.affy function?
Microarray Survival Cancer genefilter affy simpleaffy affyio Microarray Survival Cancer
17.3 years ago k. brand ▴ 420
0
votes
4
replies
1.5k
views
Problems with the size of the plots obtained with AffyPLM
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 17.3 years ago by ▴ 550 • written 17.3 years ago by ▴ 350
50 results • Page 1 of 1
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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
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Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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