Showing : affyPLM • reset
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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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10
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1.7k
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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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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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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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2
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objects masked from packages
affyPLM affyPLM
updated 14.3 years ago by 65k • written 14.3 years ago by ★ 1.5k
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2
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AffyPLM
affyPLM affyPLM
updated 20.2 years ago by ▴ 940 • written 20.3 years ago by ▴ 50
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2
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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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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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3
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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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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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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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3
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views
Images from exon arrays
affy affyPLM affy affyPLM
13.7 years ago • updated 13.6 years ago Popovic, Jelena ▴ 20
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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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votes
2
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885
views
loading affyPLM with R 2.4.
affyPLM affyPLM
updated 17.7 years ago by ★ 1.2k • written 17.7 years ago by ▴ 20
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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
0
votes
3
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915
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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votes
2
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962
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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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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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
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12
replies
1.9k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 17.5 years ago by ★ 5.5k • written 17.5 years ago by ▴ 460
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votes
9
replies
1.8k
views
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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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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3
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1.2k
views
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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4
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1.7k
views
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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1.1k
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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1
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1.3k
views
[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 17.8 years ago by ★ 7.4k • written 17.8 years ago by ★ 2.2k
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1
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880
views
qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 17.7 years ago by 65k • written 17.7 years ago by ▴ 10
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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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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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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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1
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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
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6
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1.1k
views
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
0
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1
reply
989
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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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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1.1k
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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5
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2.4k
views
error in ls() unused arguments
mouse4302 affyPLM mouse4302 affyPLM
updated 15.3 years ago by ★ 2.3k • written 15.3 years ago by ▴ 40
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votes
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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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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votes
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
0
votes
1
reply
715
views
reference on package affyPLM, fitPLM
affyPLM affyPLM
19.6 years ago Fangxin Hong ▴ 810
0
votes
1
reply
951
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
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3
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1.1k
views
AffyPLM
affyPLM affyPLM
18.8 years ago lucia ¿? ▴ 50
0
votes
2
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1.3k
views
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
0
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1
reply
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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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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votes
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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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
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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
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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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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
50 results • Page 1 of 1
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Replies
Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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