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
6.7 years ago Guido Hooiveld ★ 3.6k
1
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733
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affyPLM boxplots for subset of samples
affyPLM
updated 6.9 years ago by 63k • written 6.9 years ago by ▴ 360
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1.0k
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NUSE lmFit fitPLM
Microarray limma affyPLM
updated 7.4 years ago by 47k • written 11.1 years ago by ▴ 10
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1
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2.0k
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Computing NUSE and RLE scores
affyPLM RLE NUSE
updated 8.3 years ago by 21k • written 8.3 years ago by ▴ 10
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3
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1.1k
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Is a subset of my arrays from degraded RNA?
Microarray GO Clustering affy affyPLM simpleaffy Microarray GO Clustering affy affyPLM
8.9 years ago Peter Davidsen ▴ 210
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4
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1.2k
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affyPLM crashing R
affyPLM Harshlight affyPLM Harshlight
updated 9.5 years ago by 13k • written 9.5 years ago by ★ 12k
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2
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768
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Saving all AffyPLM residual plots to disk
affyPLM affyPLM
updated 9.7 years ago by 63k • written 9.7 years ago by ▴ 90
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1.2k
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SCAN.UPC vs NUSE
affy affyPLM SCAN.UPC affy affyPLM SCAN.UPC
updated 9.7 years ago by ▴ 590 • written 9.7 years ago by ▴ 10
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1.1k
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package \"affyPLM\" install errors on linux
affyPLM affyPLM
updated 9.9 years ago by 6.6k • written 9.9 years ago by ★ 12k
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3
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1.8k
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arrayQualityMetrics error on windows
affyPLM affyPLM
10.8 years ago Marcus Davy ▴ 390
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5
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777
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how to rank affy probesets by their probe-effect magnitude
probe affy affyPLM probe affy affyPLM
updated 11.2 years ago by 63k • written 11.2 years ago by ★ 3.0k
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0
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1.1k
views
arrayQualityMetrics package - bugs and errors
limma affyPLM convert arrayQualityMetrics limma affyPLM convert arrayQualityMetrics
11.3 years ago Wolfgang Huber 13k
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4
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1.4k
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arrayQualityMetrics package - bugs and errors
limma affyPLM arrayQualityMetrics limma affyPLM arrayQualityMetrics
updated 11.3 years ago by 13k • written 11.3 years ago by ▴ 90
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4
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955
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MA plots for large number of arrays
affy affyPLM beadarray lumi affy affyPLM beadarray lumi
updated 11.6 years ago by ▴ 720 • written 11.6 years ago by ▴ 360
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741
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bitmap() extremely slow!
Microarray affyPLM Microarray affyPLM
12.1 years ago Groot, Philip de ▴ 630
0
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3
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830
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Images from exon arrays
affy affyPLM affy affyPLM
12.7 years ago Popovic, Jelena ▴ 20
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1
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743
views
Quality control on Human Affymetrix Exon microarrays
affyPLM xps affyPLM xps
updated 12.7 years ago by ★ 3.9k • written 12.7 years ago by ▴ 120
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3
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1.2k
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identical output plots for NUSE AND RLE
GO Cancer affyPLM GO Cancer affyPLM
updated 13.0 years ago by ▴ 320 • written 13.0 years ago by ★ 2.0k
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601
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Loading workspace blocks generic function dispach
affyPLM affyPLM
13.0 years ago Eric Blanc ▴ 10
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714
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Problems in MAplot for affybatch objects
affy affyPLM affy affyPLM
13.1 years ago Ben Bolstad ★ 1.2k
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696
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Affy exon array equivalents of QC packages (affyPLM, arrayQualityMetrics & affyQCReport)
Cancer affyPLM affyQCReport arrayQualityMetrics Cancer affyPLM affyQCReport
13.1 years ago Daniel Brewer ★ 1.9k
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667
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Accessing median and IQR values of MAplots
affyPLM affyPLM
13.2 years ago Javier Pérez Florido ▴ 840
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2
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1.0k
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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 13.3 years ago by ★ 1.2k • written 13.3 years ago by ★ 4.3k
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2
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1.2k
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objects masked from packages
affyPLM affyPLM
updated 13.3 years ago by 63k • written 13.3 years ago by ★ 1.5k
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2
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960
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ArrayQualityMetrics: Problem with labels in plots. A bug??
affyPLM arrayQualityMetrics affyPLM arrayQualityMetrics
updated 13.6 years ago by ▴ 280 • written 13.6 years ago by ▴ 40
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880
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affyPLM QC vignette is missing...
probe Biobase affy gcrma matchprobes affyPLM probe Biobase affy gcrma matchprobes
14.3 years ago Jenny Drnevich ★ 2.0k
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5
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2.0k
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error in ls() unused arguments
mouse4302 affyPLM mouse4302 affyPLM
updated 14.3 years ago by ★ 2.3k • written 14.3 years ago by ▴ 40
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4
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1.2k
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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 14.5 years ago by 63k • written 14.5 years ago by ▴ 130
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743
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spiked controls wrong order on samples wit 2 rounds of amplification normalize with GCRMA
Microarray Cancer affy gcrma affyPLM Microarray Cancer affy gcrma affyPLM
14.7 years ago Richard Friedman ★ 2.0k
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10
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1.2k
views
exonmap RMA function
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap
updated 15.4 years ago by ▴ 250 • written 15.4 years ago by 25k
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871
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MTP error
GO Survival multtest affy affydata annaffy affyPLM affyio GO Survival multtest affy
15.6 years ago Boel Brynedal ▴ 200
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1
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782
views
affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 15.7 years ago by ★ 1.2k • written 15.7 years ago by ★ 2.4k
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0
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899
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Questions about Affymetrix E. Coli arrays
Normalization Cancer affy gcrma affyPLM Normalization Cancer affy gcrma affyPLM
15.8 years ago Jenny Drnevich ★ 2.2k
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5
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1.5k
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affyPLM - cant plot chip pseudo image
cdf genefilter affy affydata affyPLM simpleaffy affyio cdf genefilter affy affydata
updated 15.9 years ago by 63k • written 15.9 years ago by ▴ 50
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824
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Return of "I'm sorry, I do not know about chip type (foo)"
Survival cdf affydata limma gcrma matchprobes affyPLM simpleaffy Survival cdf affydata
15.9 years ago Dave Jacoby ▴ 20
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0
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740
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Normalization of 2 color Nimblegen array
cdf affy affyPLM convert oligo makePlatformDesign cdf affy affyPLM convert oligo
16.0 years ago dhruv pant ▴ 30
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9
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1.4k
views
problem with duplicateCorrelation and ExpressionSet objects
GO Survival cdf Biobase graph limma gcrma annaffy affyPLM simpleaffy biomaRt Category
updated 16.0 years ago by ★ 7.4k • written 16.1 years ago by ★ 2.2k
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4
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1.4k
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affyPLM and exon array question
cdf affy makecdfenv affyPLM cdf affy makecdfenv affyPLM
updated 16.1 years ago by ★ 1.2k • written 16.1 years ago by ▴ 30
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2
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1.4k
views
"AveExp" column has dissappeared from limma topTable
GO Survival annotate geneplotter affydata limma annaffy affyPLM GO Survival annotate
updated 16.2 years ago by 47k • written 16.2 years ago by ▴ 680
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0
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833
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Analysis with MBNI re-mapped (custom) CDF files
Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe
16.3 years ago Richard Pearson ▴ 390
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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 16.4 years ago by ▴ 550 • written 16.4 years ago by ▴ 350
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11
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2.2k
views
trouble hacking plotPCA
GO Survival Biobase genefilter affy affydata graph limma gcrma matchprobes affyPLM RBGL
updated 16.5 years ago by ▴ 10 • written 16.5 years ago by ★ 2.2k
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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 16.5 years ago by 13k • written 16.5 years ago by ▴ 510
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12
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1.5k
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Some Genefilter questions
GO Survival cdf genefilter geneplotter tkWidgets affy affydata widgetTools gcrma affyPLM
updated 16.5 years ago by ★ 5.5k • written 16.5 years ago by ▴ 460
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2
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2.6k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 16.5 years ago by ★ 7.4k • written 16.5 years ago by ▴ 360
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2
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877
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 16.7 years ago by ★ 1.2k • written 16.7 years ago by ▴ 420
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736
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method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
16.7 years ago k. brand ▴ 420
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2
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706
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normalize.quantiles.robust: how to implement weights for different arrays?
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio
updated 16.7 years ago by 6.5k • written 16.7 years ago by ▴ 420
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749
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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
16.7 years ago k. brand ▴ 420
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2
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668
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loading affyPLM with R 2.4.
affyPLM affyPLM
updated 16.8 years ago by ★ 1.2k • written 16.8 years ago by ▴ 20
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Comment: Use with_go along with other filters in getBM function by RuBBiT0 ▴ 10
Thank you! I think that makes much sense to me.
Comment: Interpret plot from DiffBind by Rory Stark ★ 4.8k
Not necessarily. It look to me like there is reconfiguring going on, with some chromatin that was open in the control becoming closed (the …
Comment: Interpret plot from DiffBind by Chris • 0
Thanks Rory! So that means the diseased sample has chromatin more open then the control one, is that correct?
Answer: List of Deprecated Packages for Bioc3.17 by shepherl 3.5k
lfa and gcatest have been reinstated.
Comment: Remove duplicate genera in DEseq output? by Lluís Revilla Sancho ▴ 710
How is your data before calculating the deg_DESeq? I see you use `phyloseq_to_deseq2` which should work well, but have you double checked t…
Votes
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
A: Generating a proper TxDb instance from NCBI GFF Annotations File
A: VariantAnnotation non-model species
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