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
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1.2k
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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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1.4k
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NUSE lmFit fitPLM
Microarray limma affyPLM
updated 8.8 years ago by 51k • written 12.6 years ago by ▴ 10
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2.5k
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Computing NUSE and RLE scores
affyPLM RLE NUSE
updated 9.8 years ago by 21k • written 9.8 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
10.3 years ago Peter Davidsen ▴ 210
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4
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1.6k
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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 11.1 years ago by 67k • written 11.1 years ago by ▴ 90
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2
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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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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
views
arrayQualityMetrics error on windows
affyPLM affyPLM
12.2 years ago Marcus Davy ▴ 390
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5
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1.3k
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how to rank affy probesets by their probe-effect magnitude
probe affy affyPLM probe affy affyPLM
updated 12.7 years ago by 67k • written 12.7 years ago by ★ 3.4k
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1.4k
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arrayQualityMetrics package - bugs and errors
limma affyPLM convert arrayQualityMetrics limma affyPLM convert arrayQualityMetrics
12.7 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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1.0k
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bitmap() extremely slow!
Microarray affyPLM Microarray affyPLM
13.5 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
14.2 years ago • updated 14.1 years ago Popovic, Jelena ▴ 20
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1.1k
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Quality control on Human Affymetrix Exon microarrays
affyPLM xps affyPLM xps
updated 14.2 years ago by ★ 3.9k • written 14.2 years ago by ▴ 120
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3
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identical output plots for NUSE AND RLE
GO Cancer affyPLM GO Cancer affyPLM
updated 14.4 years ago by ▴ 320 • written 14.4 years ago by ★ 2.0k
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869
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Loading workspace blocks generic function dispach
affyPLM affyPLM
14.4 years ago Eric Blanc ▴ 10
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1.0k
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Problems in MAplot for affybatch objects
affy affyPLM affy affyPLM
14.5 years ago Ben Bolstad ★ 1.2k
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947
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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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915
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Accessing median and IQR values of MAplots
affyPLM affyPLM
14.6 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 14.7 years ago by ★ 1.2k • written 14.7 years ago by ★ 4.3k
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2
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1.6k
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objects masked from packages
affyPLM affyPLM
updated 14.8 years ago by 67k • written 14.8 years ago by ★ 1.5k
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2
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1.3k
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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
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affyPLM QC vignette is missing...
probe Biobase affy gcrma matchprobes affyPLM probe Biobase affy gcrma matchprobes
15.7 years ago Jenny Drnevich ★ 2.0k
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5
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2.6k
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error in ls() unused arguments
mouse4302 affyPLM mouse4302 affyPLM
updated 15.8 years ago by ★ 2.3k • written 15.8 years ago by ▴ 40
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4
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1.6k
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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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988
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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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2.0k
views
exonmap RMA function
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap
updated 16.8 years ago by ▴ 250 • written 16.8 years ago by 25k
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0
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1.2k
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
17.0 years ago Boel Brynedal ▴ 200
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1
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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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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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2.1k
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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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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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1.1k
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
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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 17.5 years ago by ★ 7.4k • written 17.5 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 17.6 years ago by 51k • written 17.6 years ago by ▴ 680
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Analysis with MBNI re-mapped (custom) CDF files
Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe
17.8 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 17.8 years ago by ▴ 550 • written 17.8 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 17.9 years ago by ▴ 10 • written 17.9 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 17.9 years ago by ★ 13k • written 17.9 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 18.0 years ago by ★ 5.5k • written 18.0 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 18.0 years ago by ★ 7.4k • written 18.0 years ago by ▴ 360
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2
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1.3k
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"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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1.1k
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
18.2 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 18.2 years ago by ★ 6.5k • written 18.1 years ago by ▴ 420
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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
18.2 years ago k. brand ▴ 420
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2
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1000
views
loading affyPLM with R 2.4.
affyPLM affyPLM
updated 18.2 years ago by ★ 1.2k • written 18.2 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
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Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
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