Showing : affyplm • reset
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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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11
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2.7k
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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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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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1.8k
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problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 17.0 years ago by ★ 7.4k • written 17.0 years ago by ★ 2.2k
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8
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1.9k
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Biological replication (was RNA degradation problem)
Normalization probe affy affyPLM Normalization probe affy affyPLM
18.3 years ago Naomi Altman ★ 6.0k
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6
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1.1k
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What wrong with my data using LIMMA
Microarray affy limma affyPLM Microarray affy limma affyPLM
updated 18.7 years ago by ★ 1.8k • written 18.7 years ago by 50k
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5
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2.4k
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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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5
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1.9k
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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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5
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1.1k
views
how to rank affy probesets by their probe-effect magnitude
probe affy affyPLM probe affy affyPLM
updated 12.2 years ago by 65k • written 12.2 years ago by ★ 3.3k
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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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4
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1.1k
views
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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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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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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1.5k
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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4
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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
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3
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1.2k
views
Install of 1.5 Packages fails
GO edd genefilter annaffy affyPLM marray GO edd genefilter annaffy affyPLM marray
updated 19.5 years ago by ★ 5.5k • written 19.5 years ago by ★ 1.7k
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3
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1.2k
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LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 18.7 years ago by 50k • written 18.7 years ago by ▴ 270
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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 13.9 years ago by ▴ 320 • written 13.9 years ago by ★ 2.0k
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3
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1.1k
views
Images from exon arrays
affy affyPLM affy affyPLM
13.6 years ago Popovic, Jelena ▴ 20
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3
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1.1k
views
AffyPLM
affyPLM affyPLM
18.8 years ago lucia ¿? ▴ 50
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3
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2.1k
views
arrayQualityMetrics error on windows
affyPLM affyPLM
11.7 years ago Marcus Davy ▴ 390
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3
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1.3k
views
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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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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3
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909
views
Error messages in affylmGUI on PC with respect to plotting
limma affyPLM affylmGUI limma affyPLM affylmGUI
18.8 years ago Seth Falcon ★ 7.4k
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2
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957
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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2
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1.1k
views
AffyPLM
affyPLM affyPLM
updated 20.2 years ago by ▴ 940 • written 20.2 years ago by ▴ 50
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2
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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
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2
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1.5k
views
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
0
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2
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1.0k
views
Saving all AffyPLM residual plots to disk
affyPLM affyPLM
updated 10.6 years ago by 65k • written 10.6 years ago by ▴ 90
0
votes
2
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884
views
loading affyPLM with R 2.4.
affyPLM affyPLM
updated 17.7 years ago by ★ 1.2k • written 17.7 years ago by ▴ 20
0
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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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1.3k
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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1.2k
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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2
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1.2k
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Re: how to evaluate the arrays quality?
GO affy affyPLM GO affy affyPLM
updated 18.9 years ago by ▴ 110 • written 18.9 years ago by ▴ 350
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2
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1.3k
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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
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2
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1.3k
views
gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 19.5 years ago by ★ 7.4k • written 19.5 years ago by ▴ 130
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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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2
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2.9k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 17.5 years ago by ★ 7.4k • written 17.5 years ago by ▴ 360
0
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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
1
vote
1
reply
2.3k
views
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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1
reply
1.1k
views
Problems with packages: annaffy, GO, KEGG, golubEsets
GO edd annaffy affyPLM GO edd annaffy affyPLM
updated 19.4 years ago by ★ 5.5k • written 19.4 years ago by ▴ 10
0
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1
reply
1.1k
views
RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 18.3 years ago by ▴ 810 • written 18.3 years ago by ▴ 940
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1
reply
1.1k
views
affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 19.8 years ago by ▴ 1000 • written 19.8 years ago by ▴ 60
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1
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1.4k
views
Bioconductor 1.4 released
Proteomics Annotation Normalization GO Cancer CGH pamr gcrma gpls affyPLM webbioc bim
updated 20.0 years ago by ★ 13k • written 20.0 years ago by ▴ 810
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1
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1.2k
views
NUSE lmFit fitPLM
Microarray limma affyPLM
updated 8.3 years ago by 50k • written 12.1 years ago by ▴ 10
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1
reply
1.3k
views
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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votes
1
reply
988
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
0
votes
1
reply
947
views
Quality control on Human Affymetrix Exon microarrays
affyPLM xps affyPLM xps
updated 13.7 years ago by ★ 3.9k • written 13.7 years ago by ▴ 120
1
vote
1
reply
1000
views
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
reply
1.3k
views
[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 17.7 years ago by ★ 7.4k • written 17.7 years ago by ★ 2.2k
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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Comment: Too many significant genes when integrating gtex and tcga
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