Showing : affyPLM • reset
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8
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Biological replication (was RNA degradation problem)
Normalization probe affy affyPLM Normalization probe affy affyPLM
17.2 years ago Naomi Altman ★ 6.0k
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10
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1.2k
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exonmap RMA function
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap
updated 15.2 years ago by ▴ 250 • written 15.2 years ago by 25k
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5
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1.5k
views
affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 15.7 years ago by 62k • written 15.7 years ago by ▴ 50
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11
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2.1k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 16.3 years ago by ▴ 10 • written 16.3 years ago by ★ 2.2k
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2
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1.2k
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objects masked from packages
affyPLM affyPLM
updated 13.1 years ago by 62k • written 13.1 years ago by ★ 1.5k
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2
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740
views
AffyPLM
affyPLM affyPLM
updated 19.1 years ago by ▴ 940 • written 19.1 years ago by ▴ 50
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2
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863
views
Re: how to evaluate the arrays quality?
GO affy affyPLM GO affy affyPLM
updated 17.8 years ago by ▴ 110 • written 17.8 years ago by ▴ 350
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2
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1.0k
views
gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 18.4 years ago by ★ 7.4k • written 18.4 years ago by ▴ 130
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3
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1.2k
views
identical output plots for NUSE AND RLE
GO Cancer affyPLM GO Cancer affyPLM
updated 12.8 years ago by ▴ 320 • written 12.8 years ago by ★ 2.0k
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4
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1.4k
views
arrayQualityMetrics package - bugs and errors
limma affyPLM arrayQualityMetrics limma affyPLM arrayQualityMetrics
updated 11.1 years ago by 13k • written 11.1 years ago by ▴ 90
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votes
2
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1.3k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 16.0 years ago by 47k • written 16.0 years ago by ▴ 680
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3
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796
views
Images from exon arrays
affy affyPLM affy affyPLM
12.5 years ago Popovic, Jelena ▴ 20
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4
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1.2k
views
Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder
Annotation cdf probe affy affyPLM Annotation cdf probe affy affyPLM
updated 14.3 years ago by 62k • written 14.3 years ago by ▴ 130
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2
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649
views
loading affyPLM with R 2.4.
affyPLM affyPLM
updated 16.6 years ago by ★ 1.2k • written 16.6 years ago by ▴ 20
0
votes
3
replies
870
views
Install of 1.5 Packages fails
GO edd genefilter annaffy affyPLM marray GO edd genefilter annaffy affyPLM marray
updated 18.4 years ago by ★ 5.5k • written 18.4 years ago by ★ 1.7k
0
votes
3
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654
views
Error messages in affylmGUI on PC with respect to plotting
limma affyPLM affylmGUI limma affyPLM affylmGUI
17.7 years ago Seth Falcon ★ 7.4k
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votes
2
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681
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio
updated 16.5 years ago by 6.5k • written 16.5 years ago by ▴ 420
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4
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920
views
MA plots for large number of arrays
affy affyPLM beadarray lumi affy affyPLM beadarray lumi
updated 11.4 years ago by ▴ 720 • written 11.4 years ago by ▴ 360
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2
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2.5k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 16.3 years ago by ★ 7.4k • written 16.3 years ago by ▴ 360
0
votes
12
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1.4k
views
Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 16.3 years ago by ★ 5.5k • written 16.3 years ago by ▴ 460
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votes
9
replies
1.3k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 15.8 years ago by ★ 7.4k • written 15.9 years ago by ★ 2.2k
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5
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747
views
how to rank affy probesets by their probe-effect magnitude
probe affy affyPLM probe affy affyPLM
updated 11.1 years ago by 62k • written 11.1 years ago by ★ 3.0k
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3
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936
views
LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 17.6 years ago by 47k • written 17.6 years ago by ▴ 270
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4
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1.3k
views
affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 15.9 years ago by ★ 1.2k • written 15.9 years ago by ▴ 30
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2
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874
views
median of the NUSE value
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 16.8 years ago by ★ 1.2k • written 16.8 years ago by ▴ 270
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1
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1.0k
views
[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 16.6 years ago by ★ 7.4k • written 16.6 years ago by ★ 2.2k
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1
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750
views
qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 16.6 years ago by 62k • written 16.6 years ago by ▴ 10
0
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2
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851
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 16.5 years ago by ★ 1.2k • written 16.5 years ago by ▴ 420
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3
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1.8k
views
arrayQualityMetrics error on windows
affyPLM affyPLM
10.6 years ago Marcus Davy ▴ 390
0
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4
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1.1k
views
Problems with the size of the plots obtained with AffyPLM
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 16.2 years ago by ▴ 550 • written 16.2 years ago by ▴ 350
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1
reply
914
views
Problems with packages: annaffy, GO, KEGG, golubEsets
GO edd annaffy affyPLM GO edd annaffy affyPLM
updated 18.3 years ago by ★ 5.5k • written 18.3 years ago by ▴ 10
0
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6
replies
751
views
What wrong with my data using LIMMA
Microarray affy limma affyPLM Microarray affy limma affyPLM
updated 17.6 years ago by ★ 1.8k • written 17.6 years ago by 47k
0
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1
reply
760
views
affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 15.5 years ago by ★ 1.2k • written 15.5 years ago by ★ 2.4k
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1
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1.1k
views
Bioconductor 1.4 released
Proteomics Annotation Normalization GO Cancer CGH pamr gcrma gpls affyPLM webbioc bim
updated 18.9 years ago by 13k • written 18.9 years ago by ▴ 810
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1
reply
877
views
affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 18.7 years ago by ▴ 1000 • written 18.7 years ago by ▴ 60
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5
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2.0k
views
error in ls() unused arguments
mouse4302 affyPLM mouse4302 affyPLM
updated 14.1 years ago by ★ 2.3k • written 14.1 years ago by ▴ 40
0
votes
1
reply
824
views
RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 17.2 years ago by ▴ 810 • written 17.2 years ago by ▴ 940
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2
replies
936
views
ArrayQualityMetrics: Problem with labels in plots. A bug??
affyPLM arrayQualityMetrics affyPLM arrayQualityMetrics
updated 13.4 years ago by ▴ 280 • written 13.4 years ago by ▴ 40
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2
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1.0k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Annotation Normalization Preprocessing cdf probe affy affyPLM oligo Microarray
updated 13.1 years ago by ★ 1.2k • written 13.1 years ago by ★ 4.3k
0
votes
1
reply
578
views
reference on package affyPLM, fitPLM
affyPLM affyPLM
18.5 years ago Fangxin Hong ▴ 810
0
votes
1
reply
712
views
Quality control on Human Affymetrix Exon microarrays
affyPLM xps affyPLM xps
updated 12.5 years ago by ★ 3.9k • written 12.5 years ago by ▴ 120
0
votes
3
replies
764
views
AffyPLM
affyPLM affyPLM
17.7 years ago lucia ¿? ▴ 50
0
votes
2
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1.0k
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 16.8 years ago by ▴ 50 • written 16.8 years ago by ▴ 20
0
votes
1
reply
978
views
NUSE lmFit fitPLM
Microarray limma affyPLM
updated 7.2 years ago by 47k • written 11.0 years ago by ▴ 10
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3
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1.3k
views
ExpressionSet, fitPLM confusion
cdf probe gcrma matchprobes affyPLM affyio cdf probe gcrma matchprobes affyPLM affyio
updated 16.3 years ago by 13k • written 16.3 years ago by ▴ 510
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1
reply
1.0k
views
package \"affyPLM\" install errors on linux
affyPLM affyPLM
updated 9.7 years ago by 6.6k • written 9.7 years ago by ★ 12k
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2
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1.2k
views
SCAN.UPC vs NUSE
affy affyPLM SCAN.UPC affy affyPLM SCAN.UPC
updated 9.5 years ago by ▴ 590 • written 9.5 years ago by ▴ 10
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votes
2
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753
views
Saving all AffyPLM residual plots to disk
affyPLM affyPLM
updated 9.5 years ago by 62k • written 9.5 years ago by ▴ 90
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4
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1.1k
views
affyPLM crashing R
affyPLM Harshlight affyPLM Harshlight
updated 9.3 years ago by 13k • written 9.3 years ago by ★ 12k
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3
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1.1k
views
Is a subset of my arrays from degraded RNA?
Microarray GO Clustering affy affyPLM simpleaffy Microarray GO Clustering affy affyPLM
8.7 years ago Peter Davidsen ▴ 210
50 results • Page 1 of 1
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Comment: Merging samples from different sequencing runs by Zainab • 0
Thanks Michael! I've included the factors of unwanted variation to get the PCA plot on the right. Is that a suitable approach to combine re…
Comment: How to adjust plots generated using psygenet2r? by helucro ▴ 70
It's a base R plot, so you can not modify it post-generation. Running the `psygenetGene` doc example... ``` library(psygenet2r) data(qr, pa…
Comment: Multifactorial Design for DESEQ2 by ATpoint ★ 2.4k
There is a section in the vignette that covers interactions and (depending on use case) how one can do a full factorial design to make inte…
Answer: Multifactorial Design for DESEQ2 by Michael Love 39k
For questions about the experimental design, I recommend to consult with a local statistician. I have to reserve my time on the support sit…
Answer: Merging samples from different sequencing runs by Michael Love 39k
We often use RUV in the lab, and you would include the factors of unwanted variation in the design formula. See the workflow for example co…
Votes
A: Deseq2: RNA-seq and Negative binomial distribution
A: DESeq2 and shrinkage of log2 fold changes
Filtering low variance genes for WGCNA
Calculation of module membership in WGCNA
A: converting ensembl transcript ID to ensemble gene: problem & missing values
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