Showing : affyPLM • reset
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Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 360
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11
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trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 16.8 years ago by ▴ 10 • written 16.8 years ago by ★ 2.2k
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error in ls() unused arguments
mouse4302 affyPLM mouse4302 affyPLM
updated 14.7 years ago by ★ 2.3k • written 14.7 years ago by ▴ 40
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2.1k
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Computing NUSE and RLE scores
affyPLM RLE NUSE
updated 8.6 years ago by 21k • written 8.6 years ago by ▴ 10
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3
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1.9k
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arrayQualityMetrics error on windows
affyPLM affyPLM
11.1 years ago Marcus Davy ▴ 390
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5
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 16.2 years ago by 63k • written 16.2 years ago by ▴ 50
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 16.8 years ago by ★ 5.5k • written 16.8 years ago by ▴ 460
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8
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Biological replication (was RNA degradation problem)
Normalization probe affy affyPLM Normalization probe affy affyPLM
17.7 years ago Naomi Altman ★ 6.0k
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problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 16.4 years ago by ★ 7.4k • written 16.4 years ago by ★ 2.2k
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4
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arrayQualityMetrics package - bugs and errors
limma affyPLM arrayQualityMetrics limma affyPLM arrayQualityMetrics
updated 11.6 years ago by 13k • written 11.6 years ago by ▴ 90
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affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 16.4 years ago by ★ 1.2k • written 16.4 years ago by ▴ 30
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"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 16.5 years ago by 48k • written 16.5 years ago by ▴ 680
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3
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ExpressionSet, fitPLM confusion
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio
updated 16.8 years ago by 13k • written 16.8 years ago by ▴ 510
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10
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1.4k
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exonmap RMA function
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap
updated 15.7 years ago by ▴ 250 • written 15.7 years ago by 25k
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identical output plots for NUSE AND RLE
GO Cancer affyPLM GO Cancer affyPLM
updated 13.3 years ago by ▴ 320 • written 13.3 years ago by ★ 2.0k
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4
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affyPLM crashing R
affyPLM Harshlight affyPLM Harshlight
updated 9.8 years ago by 13k • written 9.8 years ago by ★ 12k
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4
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1.3k
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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 14.8 years ago by 63k • written 14.8 years ago by ▴ 130
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4
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1.3k
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Problems with the size of the plots obtained with AffyPLM
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 16.7 years ago by ▴ 550 • written 16.7 years ago by ▴ 350
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2
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SCAN.UPC vs NUSE
affy affyPLM SCAN.UPC affy affyPLM SCAN.UPC
updated 10.0 years ago by ▴ 590 • written 10.0 years ago by ▴ 10
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2
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1.3k
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objects masked from packages
affyPLM affyPLM
updated 13.6 years ago by 63k • written 13.6 years ago by ★ 1.5k
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0
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1.2k
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NA values
Normalization Cancer limma gcrma affyPLM limmaGUI plier Normalization Cancer limma gcrma
18.2 years ago Brooke-Powell, Elizabeth ▴ 170
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1.2k
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Bioconductor 1.4 released
Proteomics Annotation Normalization GO Cancer CGH pamr gcrma gpls affyPLM webbioc bim
updated 19.4 years ago by 13k • written 19.4 years ago by ▴ 810
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arrayQualityMetrics package - bugs and errors
limma affyPLM convert arrayQualityMetrics limma affyPLM convert arrayQualityMetrics
11.6 years ago Wolfgang Huber 13k
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2
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gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 18.9 years ago by ★ 7.4k • written 18.9 years ago by ▴ 130
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1
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1.1k
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package \"affyPLM\" install errors on linux
affyPLM affyPLM
updated 10.2 years ago by 6.7k • written 10.2 years ago by ★ 12k
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3
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Is a subset of my arrays from degraded RNA?
Microarray GO Clustering affy affyPLM simpleaffy Microarray GO Clustering affy affyPLM
9.2 years ago Peter Davidsen ▴ 210
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1
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[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 17.1 years ago by ★ 7.4k • written 17.1 years ago by ★ 2.2k
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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 17.3 years ago by ▴ 50 • written 17.3 years ago by ▴ 20
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2
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RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Annotation Normalization Preprocessing cdf probe affy affyPLM oligo Microarray
updated 13.6 years ago by ★ 1.2k • written 13.6 years ago by ★ 4.3k
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affy packages on Linux doesn't get installed
DynDoc tkWidgets affy affyPLM DynDoc tkWidgets affy affyPLM
19.9 years ago juliab@stat.berkeley.edu ▴ 10
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1.1k
views
NUSE lmFit fitPLM
Microarray limma affyPLM
updated 7.7 years ago by 48k • written 11.5 years ago by ▴ 10
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LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 18.1 years ago by 48k • written 18.1 years ago by ▴ 270
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2
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ArrayQualityMetrics: Problem with labels in plots. A bug??
affyPLM arrayQualityMetrics affyPLM arrayQualityMetrics
updated 13.9 years ago by ▴ 280 • written 13.9 years ago by ▴ 40
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1
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1.0k
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Problems with packages: annaffy, GO, KEGG, golubEsets
GO edd annaffy affyPLM GO edd annaffy affyPLM
updated 18.8 years ago by ★ 5.5k • written 18.8 years ago by ▴ 10
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4
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MA plots for large number of arrays
affy affyPLM beadarray lumi affy affyPLM beadarray lumi
updated 11.9 years ago by ▴ 720 • written 11.9 years ago by ▴ 360
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3
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Install of 1.5 Packages fails
GO edd genefilter annaffy affyPLM marray GO edd genefilter annaffy affyPLM marray
updated 18.9 years ago by ★ 5.5k • written 18.9 years ago by ★ 1.7k
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2
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AffyPLM
affyPLM affyPLM
updated 19.6 years ago by ▴ 940 • written 19.6 years ago by ▴ 50
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2
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999
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median of the NUSE value
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 17.3 years ago by ★ 1.2k • written 17.3 years ago by ▴ 270
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2
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995
views
Re: how to evaluate the arrays quality?
GO affy affyPLM GO affy affyPLM
updated 18.3 years ago by ▴ 110 • written 18.3 years ago by ▴ 350
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0
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993
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AffyPLM
affyPLM affyPLM
19.6 years ago Arne.Muller@aventis.com ▴ 620
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1
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981
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affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 19.2 years ago by ▴ 1000 • written 19.2 years ago by ▴ 60
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3
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Images from exon arrays
affy affyPLM affy affyPLM
13.0 years ago Popovic, Jelena ▴ 20
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2
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956
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 17.0 years ago by ★ 1.2k • written 17.0 years ago by ▴ 420
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0
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952
views
affyPLM QC vignette is missing...
probe Biobase affy gcrma matchprobes affyPLM probe Biobase affy gcrma matchprobes
14.6 years ago Jenny Drnevich ★ 2.0k
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Questions about Affymetrix E. Coli arrays
Normalization Cancer affy gcrma affyPLM Normalization Cancer affy gcrma affyPLM
16.1 years ago Jenny Drnevich ★ 2.2k
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remove probes - code
cdf probe affy gcrma affyPLM cdf probe affy gcrma affyPLM
18.5 years ago Ariel Chernomoretz ▴ 380
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946
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
15.9 years ago Boel Brynedal ▴ 200
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1
reply
941
views
RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 17.7 years ago by ▴ 810 • written 17.7 years ago by ▴ 940
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0
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Re: trouble installing "affy" package
Annotation GO Preprocessing Biobase affy affyPLM Annotation GO Preprocessing Biobase
19.5 years ago Debjani Bhowmick ▴ 30
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Analysis with MBNI re-mapped (custom) CDF files
Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe
16.7 years ago Richard Pearson ▴ 390
50 results • Page 1 of 1
Recent ...
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Answer: Is SeqSQC compatible with hg38? by James W. MacDonald 63k
I'll answer your question with a question. Is there any reason to believe that things like IBD or PCA or Sex checks would be dependent on t…
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of by Gregory • 0
Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …
Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles) by Dorien ▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Votes
Answer: How do I merge a list of GRanges?
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
Comment: DiffBind: dba.plotProfile(profiles)
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
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