Showing : affyplm • reset
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qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 19.1 years ago by 68k • written 19.1 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 19.2 years ago by ★ 7.4k • written 19.2 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 19.3 years ago by ★ 1.2k • written 19.3 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 19.3 years ago by ▴ 50 • written 19.3 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
19.4 years ago Jenny Drnevich ★ 2.2k
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898
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affyPLM QC Assessment problem
affy affyPLM affy affyPLM
19.4 years ago Tan, Ruimin ▴ 50
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983
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affyPLM QC
affy affyPLM affy affyPLM
19.4 years ago Tan, Ruimin ▴ 50
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645
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Sam always wants more observations
probe Biobase affy affyPLM probe Biobase affy affyPLM
19.4 years ago Charles Crane ▴ 30
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8
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2.5k
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Biological replication (was RNA degradation problem)
Normalization probe affy affyPLM Normalization probe affy affyPLM
19.7 years ago Naomi Altman ★ 6.0k
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RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 19.7 years ago by ▴ 810 • written 19.7 years ago by ▴ 940
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missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
19.8 years ago Jenny Drnevich ★ 2.2k
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MAplot in affyPLM library
affyPLM affyPLM
19.9 years ago Simon Lin ▴ 270
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3
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LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 20.1 years ago by 53k • written 20.1 years ago by ▴ 270
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6
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1.5k
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What wrong with my data using LIMMA
Microarray affy limma affyPLM Microarray affy limma affyPLM
updated 20.1 years ago by ★ 1.8k • written 20.1 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
20.2 years ago Gordon Smyth 53k
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NA values
Normalization Cancer limma gcrma affyPLM limmaGUI plier Normalization Cancer limma gcrma
20.2 years ago Brooke-Powell, Elizabeth ▴ 170
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3
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1.3k
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AffyPLM
affyPLM affyPLM
20.2 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
20.2 years ago Seth Falcon ★ 7.4k
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951
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Error messages in affylmGUI on PC with respect to plotting
Cancer limma affyPLM affylmGUI Cancer limma affyPLM affylmGUI
20.2 years ago Richard Friedman ★ 2.0k
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RMA for bad chips
Microarray Normalization affyPLM Microarray Normalization affyPLM
20.3 years ago James W. MacDonald 68k
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Re: Use of RMA in increasingly-sized datasets
Microarray affyPLM Microarray affyPLM
20.3 years ago Swati Ranade ▴ 60
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2
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1.5k
views
Re: how to evaluate the arrays quality?
GO affy affyPLM GO affy affyPLM
updated 20.3 years ago by ▴ 110 • written 20.3 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
20.5 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
20.6 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
20.6 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 20.8 years ago by ★ 5.5k • written 20.8 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 20.9 years ago by ★ 5.5k • written 20.9 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 20.9 years ago by ★ 7.4k • written 20.9 years ago by ▴ 130
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1
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898
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reference on package affyPLM, fitPLM
affyPLM affyPLM
21.0 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 21.2 years ago by ▴ 1000 • written 21.2 years ago by ▴ 60
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805
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Platform independent compiler switches - affyPLM problem
affyPLM affyPLM
21.3 years ago Claudio Lottaz ▴ 110
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0
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786
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Chip art from affyPLM
affyPLM affyPLM
21.4 years ago Ben Bolstad ★ 1.1k
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1
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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 21.4 years ago by ★ 13k • written 21.4 years ago by ▴ 810
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768
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using fitPLM weights in limma analysis
affy limma affyPLM affy limma affyPLM
21.4 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
21.4 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
21.5 years ago Debjani Bhowmick ▴ 30
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AffyPLM
affyPLM affyPLM
21.6 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
21.6 years ago Arne.Muller@aventis.com ▴ 620
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affyPLM interpretation
affyPLM DOSE affyPLM DOSE
21.6 years ago Arne.Muller@aventis.com ▴ 620
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2
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1.3k
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AffyPLM
affyPLM affyPLM
updated 21.6 years ago by ▴ 940 • written 21.7 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
21.7 years ago Yen Lin Chia ▴ 50
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0
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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
21.9 years ago juliab@stat.berkeley.edu ▴ 10
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972
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Win32 packages
Ruuid rhdf5 affyPLM RdbiPgSQL Ruuid rhdf5 affyPLM RdbiPgSQL
22.0 years ago Jeff Gentry ★ 3.9k
93 results • Page 2 of 2
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Replies
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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