Showing : affyio • reset
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Needed help on maanova fitmaanova function
affy vsn limma maanova affyio affy vsn limma maanova affyio
18.3 years ago Marcelo Laia ▴ 450
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3
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2.0k
views
beadarray package: problem with bead level data
geneplotter affy affyio beadarray quantsmooth beadarraySNP geneplotter affy affyio
updated 18.3 years ago by ▴ 40 • written 18.3 years ago by ▴ 270
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5
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2.4k
views
affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 18.3 years ago by 68k • written 18.3 years ago by ▴ 50
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1
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1.5k
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beadarray readIllumina suggestions
Microarray Annotation geneplotter affy affyio beadarray quantsmooth beadarraySNP affy
updated 18.4 years ago by ▴ 460 • written 18.4 years ago by ▴ 10
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3
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3.4k
views
ReadAffy - Error VECTOR_ELT() can only be applied to a 'list', not a 'char'
affy affyio affy affyio
updated 18.4 years ago by ★ 1.2k • written 18.4 years ago by ▴ 510
1
vote
2
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1.7k
views
se.exprs extractor question
probe affy affyio probe affy affyio
updated 18.4 years ago by ▴ 390 • written 18.4 years ago by ▴ 120
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0
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1.1k
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Fwd: limma gene symbol not avialable problem
Microarray Annotation Cancer cdf probe annotate affy affydata limma matchprobes affyio
18.4 years ago lidaof ▴ 450
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3
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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 68k • written 18.4 years ago by ▴ 450
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0
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Bioconductor web page
GO Cancer tkWidgets reposTools widgetTools simpleaffy affyQCReport affyio GO Cancer
18.4 years ago Seth Falcon ★ 7.4k
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9
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2.4k
views
problem with function rma
Normalization rat2302 cdf genefilter affy simpleaffy affyQCReport affyio Normalization
updated 18.4 years ago by ★ 7.4k • written 18.4 years ago by ▴ 80
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votes
6
replies
1.9k
views
mas5 update.default problem
hgu95av2 cdf affy affyio hgu95av2 cdf affy affyio
updated 18.4 years ago by ★ 7.4k • written 18.5 years ago by ▴ 190
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6
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2.4k
views
ReadAffy Error: new versions causing problems?
genefilter gcrma matchprobes simpleaffy affyio genefilter gcrma matchprobes simpleaffy
updated 18.4 years ago by ▴ 20 • written 18.5 years ago by ▴ 200
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0
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(no subject)
hgu95av2 cdf affy affyio hgu95av2 cdf affy affyio
18.5 years ago David Ruau ▴ 190
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votes
0
replies
739
views
Suggestions for upgrading BioC (was: ReadAffy problem)
Cancer affyio Cancer affyio
18.5 years ago Seth Falcon ★ 7.4k
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 ▴ 470 • written 18.5 years ago by 53k
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2
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1.2k
views
steps to manually build AffyBatch object
GO affy affyio GO affy affyio
updated 18.6 years ago by 21k • written 18.6 years ago by ★ 1.2k
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1
reply
1.3k
views
Normalization in davidTiling demo
Normalization GO Survival genefilter geneplotter affy vsn tilingArray affyio GO Survival
updated 18.7 years ago by ★ 13k • written 18.7 years ago by ★ 1.3k
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2
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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
18.7 years ago Mark W Kimpel ▴ 830
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8
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2.3k
views
oligo on R 2.4.1?
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO
updated 18.7 years ago by ★ 7.4k • written 18.7 years ago by ★ 2.2k
0
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0
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1.0k
views
affyio package usage
affxparser affyio affxparser affyio
18.8 years ago Seth Falcon ★ 7.4k
0
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1
reply
1.7k
views
beadarray and BeadStudio v.2.3.41
Biobase affy affyio beadarray Biobase affy affyio beadarray
updated 18.8 years ago by ▴ 320 • written 18.8 years ago by ▴ 70
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1
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2.2k
views
using simpleaffy incorrectly, or is there a problem with the read.affy function?
Microarray Survival Cancer genefilter affy simpleaffy affyio Microarray Survival Cancer
18.8 years ago k. brand ▴ 420
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4
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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 ▴ 550 • written 18.8 years ago by ▴ 350
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2
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1.2k
views
"oligo" crashes in windows XP
SNP GO affyio oligo crlmm SNP GO affyio oligo crlmm
updated 18.8 years ago by ★ 4.3k • written 18.8 years ago by ▴ 190
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0
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758
views
beadarray: problem with reading in Bead Summary Data
Biobase affy affyio beadarray Biobase affy affyio beadarray
18.8 years ago Perry Moerland ▴ 130
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2
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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 68k • written 18.9 years ago by ▴ 890
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3
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1.9k
views
ExpressionSet, fitPLM confusion
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio
updated 18.9 years ago by ★ 13k • written 18.9 years ago by ▴ 510
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1
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3.2k
views
ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 18.9 years ago by 68k • written 18.9 years ago by ▴ 510
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2
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3.4k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 19.0 years ago by ★ 7.4k • written 19.0 years ago by ▴ 360
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2
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1.8k
views
results of justPlier vs. RMA
Clustering affy plier affyio Clustering affy plier affyio
updated 19.0 years ago by ▴ 120 • written 19.0 years ago by ▴ 360
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0
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953
views
Bioconductor Digest, Vol 45, Issue 9
affy simpleaffy affyio affy simpleaffy affyio
19.0 years ago Dick Beyer ★ 1.4k
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0
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simpleaffy gives error: unable to find an inherited method for function "pData"
affy simpleaffy affyio affy simpleaffy affyio
19.0 years ago Dick Beyer ★ 1.4k
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2
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1.4k
views
beadarray example data problem
Biobase affy affyio beadarray Biobase affy affyio beadarray
19.0 years ago Keith Satterley ▴ 450
0
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3
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1.4k
views
beadarray example data problem 2
Biobase affy affyio beadarray Biobase affy affyio beadarray
19.0 years ago Martin Morgan 25k
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0
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1.2k
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problems reading Illumina files using BeadExplorer
affy widgetTools limma marray convert affyio BeadExplorer affy widgetTools limma marray
19.0 years ago Vitalina Komashko ▴ 10
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1
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1.1k
views
makePlatformDesign error
affyio oligo makePlatformDesign affyio oligo makePlatformDesign
updated 19.1 years ago by 68k • written 19.1 years ago by ▴ 20
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2
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1.7k
views
problem updating packages OCPlus and RSNper
affy limma affyio OCplus affy limma affyio OCplus
updated 19.1 years ago by 16k • written 19.1 years ago by ▴ 890
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2
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1.5k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 19.1 years ago by ★ 1.2k • written 19.1 years ago by ▴ 420
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0
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1.2k
views
method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
19.1 years ago k. brand ▴ 420
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votes
2
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1.3k
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio
updated 19.1 years ago by ★ 6.5k • written 19.1 years ago by ▴ 420
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0
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4 replicates, of 3 tissues- one good hyb (2xreps), one bad hyb (2xreps). Best way forward?
qPCR affy affydata vsn limma gcrma matchprobes affyPLM affyio BRAIN qPCR affy affydata
19.2 years ago k. brand ▴ 420
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votes
2
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2.1k
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
19.2 years ago James W. MacDonald 68k
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3
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1.4k
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 19.2 years ago by ★ 1.2k • written 19.2 years ago by ▴ 420
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2
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1.6k
views
Changing the value of sampleNames for exprSet
affy affyio affy affyio
updated 19.2 years ago by 25k • written 19.2 years ago by ▴ 110
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1
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1.1k
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 19.2 years ago by 68k • written 19.2 years ago by ▴ 10
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5
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2.3k
views
RMA and justRMA error
Cancer cdf Biobase affy gcrma affyio Cancer cdf Biobase affy gcrma affyio
19.2 years ago Aedin Culhane ▴ 510
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1
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1.3k
views
qc function missing in Linux version of simpleaffy
cdf genefilter affy affydata simpleaffy affyQCReport affyio cdf genefilter affy affydata
updated 19.3 years ago by 68k • written 19.3 years ago by ▴ 160
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2
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1.5k
views
median of the NUSE value
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 19.4 years ago by ★ 1.2k • written 19.4 years ago by ▴ 270
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2
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1.6k
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 19.4 years ago by ▴ 50 • written 19.4 years ago by ▴ 20
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0
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blocking in limma gives an estimability problem
GO hgu95av2 Ruuid multtest affy graph limma RBGL qvalue Category affyio GO hgu95av2
19.4 years ago Pedro López Romero ▴ 360
106 results • Page 2 of 3
Recent ...
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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