Showing : affyplm • reset
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 19.3 years ago by 68k • written 19.3 years ago by ▴ 10
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[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 19.3 years ago by ★ 7.4k • written 19.3 years ago by ★ 2.2k
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median of the NUSE value
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 19.5 years ago by ★ 1.2k • written 19.5 years ago by ▴ 270
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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 19.5 years ago by ▴ 50 • written 19.5 years ago by ▴ 20
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Why mm's changing after bg.adjust.gcrma?
drosgenome1 cdf Biobase reposTools affy gcrma affyPLM simpleaffy affyQCReport affyio cdf
19.5 years ago Jenny Drnevich ★ 2.2k
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923
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affyPLM QC Assessment problem
affy affyPLM affy affyPLM
19.6 years ago Tan, Ruimin ▴ 50
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1.0k
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affyPLM QC
affy affyPLM affy affyPLM
19.6 years ago Tan, Ruimin ▴ 50
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670
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Sam always wants more observations
probe Biobase affy affyPLM probe Biobase affy affyPLM
19.6 years ago Charles Crane ▴ 30
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Biological replication (was RNA degradation problem)
Normalization probe affy affyPLM Normalization probe affy affyPLM
19.9 years ago Naomi Altman ★ 6.0k
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RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 19.9 years ago by ▴ 810 • written 19.9 years ago by ▴ 940
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
20.0 years ago Jenny Drnevich ★ 2.2k
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MAplot in affyPLM library
affyPLM affyPLM
20.1 years ago Simon Lin ▴ 270
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3
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LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 20.3 years ago by 53k • written 20.3 years ago by ▴ 270
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What wrong with my data using LIMMA
Microarray affy limma affyPLM Microarray affy limma affyPLM
updated 20.3 years ago by ★ 1.8k • written 20.3 years ago by 53k
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Limma using all probes on Affy chip
Normalization probe affy limma affyPLM Normalization probe affy limma affyPLM
20.3 years ago Gordon Smyth 53k
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NA values
Normalization Cancer limma gcrma affyPLM limmaGUI plier Normalization Cancer limma gcrma
20.4 years ago Brooke-Powell, Elizabeth ▴ 170
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AffyPLM
affyPLM affyPLM
20.4 years ago lucia ¿? ▴ 50
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3
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1.2k
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Error messages in affylmGUI on PC with respect to plotting
limma affyPLM affylmGUI limma affyPLM affylmGUI
20.4 years ago Seth Falcon ★ 7.4k
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971
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Error messages in affylmGUI on PC with respect to plotting
Cancer limma affyPLM affylmGUI Cancer limma affyPLM affylmGUI
20.4 years ago Richard Friedman ★ 2.0k
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RMA for bad chips
Microarray Normalization affyPLM Microarray Normalization affyPLM
20.4 years ago James W. MacDonald 68k
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Re: Use of RMA in increasingly-sized datasets
Microarray affyPLM Microarray affyPLM
20.5 years ago Swati Ranade ▴ 60
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1.5k
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Re: how to evaluate the arrays quality?
GO affy affyPLM GO affy affyPLM
updated 20.5 years ago by ▴ 110 • written 20.5 years ago by ▴ 350
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1.2k
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remove probes - code
cdf probe affy gcrma affyPLM cdf probe affy gcrma affyPLM
20.6 years ago Ariel Chernomoretz ▴ 380
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sanity check: p-value from RMA expression estimates
Normalization probe affy affyPLM Normalization probe affy affyPLM
20.8 years ago Reiner Schulz ▴ 20
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sanity check: recipe for p-value from RMA expression estimates
Normalization probe affy affyPLM Normalization probe affy affyPLM
20.8 years ago Reiner Schulz ▴ 20
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1.4k
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Problems with packages: annaffy, GO, KEGG, golubEsets
GO edd annaffy affyPLM GO edd annaffy affyPLM
updated 21.0 years ago by ★ 5.5k • written 21.0 years ago by ▴ 10
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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 21.1 years ago by ★ 5.5k • written 21.1 years ago by ★ 1.7k
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gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 21.1 years ago by ★ 7.4k • written 21.1 years ago by ▴ 130
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913
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reference on package affyPLM, fitPLM
affyPLM affyPLM
21.2 years ago Fangxin Hong ▴ 810
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1
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1.5k
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affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 21.4 years ago by ▴ 1000 • written 21.4 years ago by ▴ 60
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829
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Platform independent compiler switches - affyPLM problem
affyPLM affyPLM
21.5 years ago Claudio Lottaz ▴ 110
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0
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814
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Chip art from affyPLM
affyPLM affyPLM
21.5 years ago Ben Bolstad ★ 1.1k
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1.8k
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Bioconductor 1.4 released
Proteomics Annotation Normalization GO Cancer CGH pamr gcrma gpls affyPLM webbioc bim
updated 21.6 years ago by ★ 13k • written 21.6 years ago by ▴ 810
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using fitPLM weights in limma analysis
affy limma affyPLM affy limma affyPLM
21.6 years ago Tom Price ▴ 20
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Interpretation of output of AffyRNAdeg and hist commands
Microarray Regression Cancer affyPLM Microarray Regression Cancer affyPLM
21.6 years ago James W. MacDonald 68k
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Re: trouble installing "affy" package
Annotation GO Preprocessing Biobase affy affyPLM Annotation GO Preprocessing Biobase
21.7 years ago Debjani Bhowmick ▴ 30
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1.3k
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AffyPLM
affyPLM affyPLM
21.8 years ago Arne.Muller@aventis.com ▴ 620
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1.1k
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Quantile Normalization on mice data
Normalization Clustering probe affyPLM Normalization Clustering probe affyPLM
21.8 years ago Arne.Muller@aventis.com ▴ 620
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affyPLM interpretation
affyPLM DOSE affyPLM DOSE
21.8 years ago Arne.Muller@aventis.com ▴ 620
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2
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1.4k
views
AffyPLM
affyPLM affyPLM
updated 21.8 years ago by ▴ 940 • written 21.8 years ago by ▴ 50
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0
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1.0k
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Quantile Normalization on mice data
affyPLM affyPLM
21.8 years ago Yen Lin Chia ▴ 50
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1.5k
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affy packages on Linux doesn't get installed
DynDoc tkWidgets affy affyPLM DynDoc tkWidgets affy affyPLM
22.0 years ago juliab@stat.berkeley.edu ▴ 10
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999
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Win32 packages
Ruuid rhdf5 affyPLM RdbiPgSQL Ruuid rhdf5 affyPLM RdbiPgSQL
22.1 years ago Jeff Gentry ★ 3.9k
93 results • Page 2 of 2
Recent ...
Replies
Comment: GOseq Probability Weight Function bad fit by ejasge.r.m • 0
When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
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