Showing : affyPLM • reset
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(strange?) memory problem when running fitPLM on a set of HTA 2.0 arrays
affyPLM fitPLM hta2.0
8.1 years ago Guido Hooiveld ★ 4.1k
1
vote
1
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1.1k
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affyPLM boxplots for subset of samples
affyPLM
updated 8.3 years ago by 67k • written 8.3 years ago by ▴ 360
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1
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1.3k
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NUSE lmFit fitPLM
Microarray limma affyPLM
updated 8.8 years ago by 51k • written 12.5 years ago by ▴ 10
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1
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2.5k
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Computing NUSE and RLE scores
affyPLM RLE NUSE
updated 9.7 years ago by 21k • written 9.7 years ago by ▴ 10
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3
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1.4k
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Is a subset of my arrays from degraded RNA?
Microarray GO Clustering affy affyPLM simpleaffy Microarray GO Clustering affy affyPLM
10.2 years ago Peter Davidsen ▴ 210
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4
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1.6k
views
affyPLM crashing R
affyPLM Harshlight affyPLM Harshlight
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ★ 13k
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2
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1.2k
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Saving all AffyPLM residual plots to disk
affyPLM affyPLM
updated 11.0 years ago by 67k • written 11.0 years ago by ▴ 90
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2
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1.6k
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SCAN.UPC vs NUSE
affy affyPLM SCAN.UPC affy affyPLM SCAN.UPC
updated 11.1 years ago by ▴ 600 • written 11.1 years ago by ▴ 10
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1
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1.4k
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package \"affyPLM\" install errors on linux
affyPLM affyPLM
updated 11.3 years ago by 6.7k • written 11.3 years ago by ★ 13k
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3
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2.2k
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arrayQualityMetrics error on windows
affyPLM affyPLM
12.1 years ago Marcus Davy ▴ 390
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5
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1.2k
views
how to rank affy probesets by their probe-effect magnitude
probe affy affyPLM probe affy affyPLM
updated 12.6 years ago by 67k • written 12.6 years ago by ★ 3.4k
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0
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1.4k
views
arrayQualityMetrics package - bugs and errors
limma affyPLM convert arrayQualityMetrics limma affyPLM convert arrayQualityMetrics
12.6 years ago Wolfgang Huber ★ 13k
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4
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1.9k
views
arrayQualityMetrics package - bugs and errors
limma affyPLM arrayQualityMetrics limma affyPLM arrayQualityMetrics
updated 12.7 years ago by ★ 13k • written 12.7 years ago by ▴ 90
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4
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1.2k
views
MA plots for large number of arrays
affy affyPLM beadarray lumi affy affyPLM beadarray lumi
updated 13.0 years ago by ▴ 740 • written 13.0 years ago by ▴ 360
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0
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990
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bitmap() extremely slow!
Microarray affyPLM Microarray affyPLM
13.4 years ago Groot, Philip de ▴ 630
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3
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1.2k
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Images from exon arrays
affy affyPLM affy affyPLM
14.1 years ago Popovic, Jelena ▴ 20
0
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1
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1.0k
views
Quality control on Human Affymetrix Exon microarrays
affyPLM xps affyPLM xps
updated 14.1 years ago by ★ 3.9k • written 14.1 years ago by ▴ 120
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3
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1.6k
views
identical output plots for NUSE AND RLE
GO Cancer affyPLM GO Cancer affyPLM
updated 14.3 years ago by ▴ 320 • written 14.3 years ago by ★ 2.0k
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852
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Loading workspace blocks generic function dispach
affyPLM affyPLM
14.4 years ago Eric Blanc ▴ 10
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0
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988
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Problems in MAplot for affybatch objects
affy affyPLM affy affyPLM
14.4 years ago Ben Bolstad ★ 1.2k
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0
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934
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Affy exon array equivalents of QC packages (affyPLM, arrayQualityMetrics & affyQCReport)
Cancer affyPLM affyQCReport arrayQualityMetrics Cancer affyPLM affyQCReport
14.5 years ago Daniel Brewer ★ 1.9k
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0
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907
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Accessing median and IQR values of MAplots
affyPLM affyPLM
14.5 years ago Javier Pérez Florido ▴ 840
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2
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1.4k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Annotation Normalization Preprocessing cdf probe affy affyPLM oligo Microarray
updated 14.6 years ago by ★ 1.2k • written 14.6 years ago by ★ 4.3k
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2
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1.5k
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objects masked from packages
affyPLM affyPLM
updated 14.7 years ago by 67k • written 14.7 years ago by ★ 1.5k
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2
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1.2k
views
ArrayQualityMetrics: Problem with labels in plots. A bug??
affyPLM arrayQualityMetrics affyPLM arrayQualityMetrics
updated 15.0 years ago by ▴ 280 • written 15.0 years ago by ▴ 40
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0
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1.1k
views
affyPLM QC vignette is missing...
probe Biobase affy gcrma matchprobes affyPLM probe Biobase affy gcrma matchprobes
15.6 years ago Jenny Drnevich ★ 2.0k
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5
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2.5k
views
error in ls() unused arguments
mouse4302 affyPLM mouse4302 affyPLM
updated 15.7 years ago by ★ 2.3k • written 15.7 years ago by ▴ 40
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4
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1.6k
views
Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder
Annotation cdf probe affy affyPLM Annotation cdf probe affy affyPLM
updated 15.9 years ago by 67k • written 15.9 years ago by ▴ 130
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0
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977
views
spiked controls wrong order on samples wit 2 rounds of amplification normalize with GCRMA
Microarray Cancer affy gcrma affyPLM Microarray Cancer affy gcrma affyPLM
16.1 years ago Richard Friedman ★ 2.0k
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10
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1.9k
views
exonmap RMA function
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap
updated 16.7 years ago by ▴ 250 • written 16.7 years ago by 25k
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0
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1.2k
views
MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
16.9 years ago Boel Brynedal ▴ 200
0
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1
reply
1.1k
views
affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 17.1 years ago by ★ 1.2k • written 17.1 years ago by ★ 2.4k
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0
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1.1k
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Questions about Affymetrix E. Coli arrays
Normalization Cancer affy gcrma affyPLM Normalization Cancer affy gcrma affyPLM
17.2 years ago Jenny Drnevich ★ 2.2k
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5
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2.0k
views
affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 17.3 years ago by 67k • written 17.3 years ago by ▴ 50
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1.1k
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Return of "I'm sorry, I do not know about chip type (foo)"
Survival cdf affydata limma gcrma matchprobes affyPLM simpleaffy Survival cdf affydata
17.3 years ago Dave Jacoby ▴ 20
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0
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1.0k
views
Normalization of 2 color Nimblegen array
cdf affy affyPLM convert oligo makePlatformDesign cdf affy affyPLM convert oligo
17.4 years ago dhruv pant ▴ 30
0
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9
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2.1k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ★ 2.2k
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4
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2.0k
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affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 17.5 years ago by ★ 1.2k • written 17.5 years ago by ▴ 30
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2
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1.8k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 17.5 years ago by 51k • written 17.5 years ago by ▴ 680
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0
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1.1k
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Analysis with MBNI re-mapped (custom) CDF files
Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe
17.7 years ago Richard Pearson ▴ 390
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4
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1.6k
views
Problems with the size of the plots obtained with AffyPLM
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 17.7 years ago by ▴ 550 • written 17.7 years ago by ▴ 350
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11
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2.9k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 17.8 years ago by ▴ 10 • written 17.8 years ago by ★ 2.2k
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3
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1.7k
views
ExpressionSet, fitPLM confusion
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio
updated 17.8 years ago by ★ 13k • written 17.8 years ago by ▴ 510
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12
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2.2k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 17.9 years ago by ★ 5.5k • written 17.9 years ago by ▴ 460
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2
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3.1k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 17.9 years ago by ★ 7.4k • written 17.9 years ago by ▴ 360
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2
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1.3k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 18.1 years ago by ★ 1.2k • written 18.1 years ago by ▴ 420
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0
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1.0k
views
method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
18.1 years ago k. brand ▴ 420
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2
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1.1k
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio
updated 18.1 years ago by ★ 6.5k • written 18.1 years ago by ▴ 420
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0
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1.0k
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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
18.1 years ago k. brand ▴ 420
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2
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987
views
loading affyPLM with R 2.4.
affyPLM affyPLM
updated 18.1 years ago by ★ 1.2k • written 18.1 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to subset voomLmFit (MArrayLM) object? by Gordon Smyth 51k
Yes, the current behaviour is absolutely intentional. It doesn't seem to me to be meaningful or useful to try to subset the EList object au…
Answer: Need help interpreting heatmaps from limma by James W. MacDonald 67k
Heatmaps don't do any comparisons. They just plot the underlying data in a matrix and color the blocks based (in your case) on the by-gene …
Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10
I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…
Answer: featureCounts fails to load annotation file by James W. MacDonald 67k
I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
Votes
Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
Awards • All
Scholar to James W. MacDonald 67k
Popular Question to Dorien ▴ 10
Popular Question to boczniak767 ▴ 740
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Hervé Pagès 16k
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