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
7.6 years ago Guido Hooiveld ★ 3.9k
1
vote
1
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991
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affyPLM boxplots for subset of samples
affyPLM
updated 7.8 years ago by 65k • written 7.8 years ago by ▴ 360
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1
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1.2k
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NUSE lmFit fitPLM
Microarray limma affyPLM
updated 8.3 years ago by 50k • written 12.0 years ago by ▴ 10
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1
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2.2k
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Computing NUSE and RLE scores
affyPLM RLE NUSE
updated 9.2 years ago by 21k • written 9.2 years ago by ▴ 10
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3
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1.3k
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Is a subset of my arrays from degraded RNA?
Microarray GO Clustering affy affyPLM simpleaffy Microarray GO Clustering affy affyPLM
9.8 years ago Peter Davidsen ▴ 210
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4
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1.5k
views
affyPLM crashing R
affyPLM Harshlight affyPLM Harshlight
updated 10.4 years ago by ★ 13k • written 10.4 years ago by ★ 13k
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2
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988
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Saving all AffyPLM residual plots to disk
affyPLM affyPLM
updated 10.6 years ago by 65k • written 10.6 years ago by ▴ 90
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2
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1.5k
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SCAN.UPC vs NUSE
affy affyPLM SCAN.UPC affy affyPLM SCAN.UPC
updated 10.6 years ago by ▴ 590 • written 10.6 years ago by ▴ 10
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1
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1.3k
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package \"affyPLM\" install errors on linux
affyPLM affyPLM
updated 10.8 years ago by 6.7k • written 10.8 years ago by ★ 13k
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3
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2.0k
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arrayQualityMetrics error on windows
affyPLM affyPLM
11.6 years ago Marcus Davy ▴ 390
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5
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1.1k
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how to rank affy probesets by their probe-effect magnitude
probe affy affyPLM probe affy affyPLM
updated 12.1 years ago by 65k • written 12.1 years ago by ★ 3.3k
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0
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1.3k
views
arrayQualityMetrics package - bugs and errors
limma affyPLM convert arrayQualityMetrics limma affyPLM convert arrayQualityMetrics
12.1 years ago Wolfgang Huber ★ 13k
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4
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1.8k
views
arrayQualityMetrics package - bugs and errors
limma affyPLM arrayQualityMetrics limma affyPLM arrayQualityMetrics
updated 12.2 years ago by ★ 13k • written 12.2 years ago by ▴ 90
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4
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1.1k
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MA plots for large number of arrays
affy affyPLM beadarray lumi affy affyPLM beadarray lumi
updated 12.5 years ago by ▴ 720 • written 12.5 years ago by ▴ 360
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894
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bitmap() extremely slow!
Microarray affyPLM Microarray affyPLM
12.9 years ago Groot, Philip de ▴ 630
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3
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1.1k
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Images from exon arrays
affy affyPLM affy affyPLM
13.6 years ago Popovic, Jelena ▴ 20
0
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1
reply
939
views
Quality control on Human Affymetrix Exon microarrays
affyPLM xps affyPLM xps
updated 13.6 years ago by ★ 3.9k • written 13.6 years ago by ▴ 120
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3
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1.5k
views
identical output plots for NUSE AND RLE
GO Cancer affyPLM GO Cancer affyPLM
updated 13.8 years ago by ▴ 320 • written 13.8 years ago by ★ 2.0k
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0
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766
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Loading workspace blocks generic function dispach
affyPLM affyPLM
13.9 years ago Eric Blanc ▴ 10
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888
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Problems in MAplot for affybatch objects
affy affyPLM affy affyPLM
14.0 years ago Ben Bolstad ★ 1.2k
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0
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851
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Affy exon array equivalents of QC packages (affyPLM, arrayQualityMetrics & affyQCReport)
Cancer affyPLM affyQCReport arrayQualityMetrics Cancer affyPLM affyQCReport
14.0 years ago Daniel Brewer ★ 1.9k
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0
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819
views
Accessing median and IQR values of MAplots
affyPLM affyPLM
14.1 years ago Javier Pérez Florido ▴ 840
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2
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1.3k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Annotation Normalization Preprocessing cdf probe affy affyPLM oligo Microarray
updated 14.2 years ago by ★ 1.2k • written 14.2 years ago by ★ 4.3k
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2
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1.4k
views
objects masked from packages
affyPLM affyPLM
updated 14.2 years ago by 65k • written 14.2 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 14.5 years ago by ▴ 280 • written 14.5 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
15.2 years ago Jenny Drnevich ★ 2.0k
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5
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2.4k
views
error in ls() unused arguments
mouse4302 affyPLM mouse4302 affyPLM
updated 15.2 years ago by ★ 2.3k • written 15.2 years ago by ▴ 40
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4
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1.4k
views
Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder
Annotation cdf probe affy affyPLM Annotation cdf probe affy affyPLM
updated 15.4 years ago by 65k • written 15.4 years ago by ▴ 130
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0
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904
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
15.6 years ago Richard Friedman ★ 2.0k
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10
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1.7k
views
exonmap RMA function
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap
updated 16.3 years ago by ▴ 250 • written 16.3 years ago by 25k
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0
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1.1k
views
MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
16.4 years ago Boel Brynedal ▴ 200
0
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1
reply
976
views
affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 16.6 years ago by ★ 1.2k • written 16.6 years ago by ★ 2.4k
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0
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1.0k
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Questions about Affymetrix E. Coli arrays
Normalization Cancer affy gcrma affyPLM Normalization Cancer affy gcrma affyPLM
16.7 years ago Jenny Drnevich ★ 2.2k
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5
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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
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1.0k
views
Return of "I'm sorry, I do not know about chip type (foo)"
Survival cdf affydata limma gcrma matchprobes affyPLM simpleaffy Survival cdf affydata
16.8 years ago Dave Jacoby ▴ 20
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0
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936
views
Normalization of 2 color Nimblegen array
cdf affy affyPLM convert oligo makePlatformDesign cdf affy affyPLM convert oligo
16.9 years ago dhruv pant ▴ 30
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9
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1.8k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ★ 2.2k
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4
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1.7k
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affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 17.0 years ago by ★ 1.2k • written 17.0 years ago by ▴ 30
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2
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1.6k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 17.1 years ago by 50k • written 17.1 years ago by ▴ 680
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0
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974
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Analysis with MBNI re-mapped (custom) CDF files
Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe
17.2 years ago Richard Pearson ▴ 390
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4
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1.4k
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
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11
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2.7k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 17.4 years ago by ▴ 10 • written 17.4 years ago by ★ 2.2k
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3
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1.5k
views
ExpressionSet, fitPLM confusion
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio
updated 17.4 years ago by ★ 13k • written 17.4 years ago by ▴ 510
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12
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1.9k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 17.4 years ago by ★ 5.5k • written 17.4 years ago by ▴ 460
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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
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2
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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
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0
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956
views
method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
17.6 years ago k. brand ▴ 420
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2
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949
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
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0
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931
views
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
17.6 years ago k. brand ▴ 420
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2
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872
views
loading affyPLM with R 2.4.
affyPLM affyPLM
updated 17.7 years ago by ★ 1.2k • written 17.7 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Answer: List of Deprecated Packages for Bioc3.19 by shepherl 3.8k
singleCellTK has been fixed and will remain in Bioconductor
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Your awnser at Cannabis orgDb solve my problems using enrichGO by far. I'm underdegree biotechnology student, and I learning bioinformatic…
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
It is indeed better. Anyway, did you notice this part in the output from `str(ortologos_filtrados)`: `$Gene.ID : int 115709372 115716460 …
Votes
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
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