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0
votes
4
replies
21k
views
Unable to find an inherited method for function ‘exprs’
Biobase GEOquery virtualArray Biobase GEOquery virtualArray
updated 10.7 years ago by ★ 13k • written 10.7 years ago by ▴ 210
2
votes
2
replies
7.9k
views
Convert Expression Set into a Matrix or Data Frame
microarray biobase affy R
updated 8.2 years ago by ▴ 760 • written 8.2 years ago by • 0
0
votes
1
reply
5.7k
views
pvca error (Error in Data$variables : $ operator is invalid for atomic vectors)
pvca biobase
updated 8.7 years ago by • 0 • written 9.0 years ago by • 0
4
votes
6
replies
5.2k
views
Proper way to build phenoData object?
limma affy biobase
updated 9.2 years ago by ★ 3.9k • written 9.2 years ago by ▴ 10
2
votes
2
replies
4.4k
views
AnnotatedDataFrame is not a defined class
annotatedDataFrame R Biobase
9.4 years ago • updated 5.8 years ago nonCodingGene ▴ 10
0
votes
1
reply
4.2k
views
R package Installation Errors
Survival Biobase affy Survival Biobase affy
updated 18.3 years ago by 25k • written 18.3 years ago by ▴ 60
2
votes
5
replies
3.8k
views
How to use t.test to select best features out of multiple features?
microarray biobase feature selection t.test R
updated 8.6 years ago by ▴ 830 • written 8.6 years ago by ▴ 10
0
votes
1
reply
3.4k
views
limma and ebayes : error message : differences in versions?
Biobase limma Biobase limma
updated 14.9 years ago by 65k • written 14.9 years ago by ▴ 40
0
votes
5
replies
3.3k
views
Error in .local(.Object, ...) : could not find function "checkClass"
Biobase Biobase
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 80
0
votes
1
reply
3.1k
views
RE : create an new AnnotatedDataFrame
Annotation Survival Yeast Biobase genefilter tkWidgets marray convert arrayMagic affyio
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 30
1
vote
3
replies
3.0k
views
How to use expression set object to select genes using different gene selection methods
microarray biobase geoquery
updated 8.6 years ago by ▴ 830 • written 8.6 years ago by ▴ 10
0
votes
1
reply
3.0k
views
Excluding columns of phenoData of ExpressionSet Data in R
microarray biobase expresiondataset r
8.6 years ago floodking • 0
0
votes
2
replies
3.0k
views
Biobase - Error: ExpressionSet
Microarray Annotation GO ExperimentData Biobase Microarray Annotation GO ExperimentData
updated 10.5 years ago by 1.6k • written 10.5 years ago by ▴ 50
1
vote
2
replies
3.0k
views
how to update feature data with different dimensions in expressionSet?
biobase eSet expressionSet
updated 7.5 years ago by 25k • written 7.5 years ago by ★ 3.9k
8
votes
2
replies
3.0k
views
exprs function - clash with dplyr
exprs dplyr Biobase
5.9 years ago Wolfgang Huber ★ 13k
0
votes
4
replies
2.9k
views
Error : package slot missing from signature for generic
Biobase lumi oligoClasses Biobase lumi oligoClasses
11.7 years ago Mark Cowley ▴ 910
0
votes
1
reply
2.8k
views
NMF installation with current R version
NMF Biobase
updated 23 months ago by 3.8k • written 23 months ago by • 0
0
votes
1
reply
2.8k
views
ReadAffy can not find function read.AnnotatedDataFrame
Biobase genefilter affydata limma simpleaffy hopach affyio Biobase genefilter affydata
updated 17.4 years ago by 65k • written 17.4 years ago by ▴ 510
0
votes
11
replies
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
0
votes
2
replies
2.6k
views
installing problem - preprocessCore, affy on linux platform
Biobase genefilter affy vsn gcrma matchprobes preprocessCore Biobase genefilter affy vsn
updated 15.6 years ago by ★ 6.5k • written 15.6 years ago by ▴ 20
0
votes
2
replies
2.6k
views
[R] Error in setMethod("combine"... was - Error when installing globaltest package
Infrastructure Cancer Biobase tkWidgets globaltest BiocInstaller BiocGenerics Cancer
updated 11.1 years ago by 25k • written 11.1 years ago by ▴ 40
2
votes
4
replies
2.4k
views
error: namespace Loading DESeq2
deseq2 error namespace biobase
updated 5.3 years ago by 65k • written 5.3 years ago by • 0
1
vote
2
replies
2.4k
views
making ExpressionSet from RGList via NChannelSet for use with 'sva'
biobase convert sva ringo arrayqualitymetrics
updated 8.1 years ago by 50k • written 8.1 years ago by • 0
0
votes
2
replies
2.4k
views
[R] Select single probe-set with median expression from multiple probe-sets corresponding to same gene -AFFY
GO probe Biobase genefilter GO probe Biobase genefilter
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 30
0
votes
5
replies
2.4k
views
Unable to install packages
Biobase Biobase
updated 12.8 years ago by ▴ 50 • written 12.8 years ago by ▴ 30
1
vote
3
replies
2.4k
views
Error installing Biobase on R 3.1.2
biobase
updated 9.2 years ago by ★ 2.0k • written 9.2 years ago by • 0
2
votes
2
replies
2.4k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray biobase
5.8 years ago charlesgwellem ▴ 10
4
votes
8
replies
2.3k
views
ALL dataset, correct syntax using the exprs call?
ALL bioconductor biobase exprs
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
0
votes
3
replies
2.3k
views
trouble installing "affy" package
Biobase tkWidgets affy Biobase tkWidgets affy
20.2 years ago Jeffrey Chang ▴ 40
4
votes
8
replies
2.2k
views
Help! ExpressionSet function from Biobase not working! (issue with data structure??)
limma biobase ExpressionSet
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
0
votes
2
replies
2.2k
views
make.cdf.package Error in copySubstitute
GO cdf Biobase affy GO cdf Biobase affy
updated 10.1 years ago by 65k • written 10.1 years ago by ▴ 30
0
votes
1
reply
2.2k
views
Example on constructing AffyBatch object
Biobase affydata Biobase affydata
updated 13.8 years ago by 65k • written 13.8 years ago by ▴ 940
0
votes
0
replies
2.1k
views
Welcome
Biobase annotate Biobase annotate
22.4 years ago rgentleman ★ 5.5k
0
votes
4
replies
2.1k
views
Installing affy package
Biobase affy Biobase affy
updated 14.4 years ago by ▴ 450 • written 14.4 years ago by ▴ 140
0
votes
7
replies
2.0k
views
S4 object??
Biobase limma Biobase limma
updated 14.5 years ago by 65k • written 14.5 years ago by ▴ 40
3
votes
4
replies
2.0k
views
R session aborted: prcomp
Biobase stats
updated 3.0 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
5
replies
2.0k
views
Install a custom CDF file
makecdf RMA annotation biobase GEOquery
updated 4.8 years ago by 65k • written 4.8 years ago by • 0
6
votes
13
replies
2.0k
views
Comparison of Column of AnnotatedDataFrame
biobase AnnotatedDataFrame
7.6 years ago Dario Strbenac ★ 1.5k
0
votes
3
replies
2.0k
views
cannot access annotation from ExpressionSet in Bioc-Devel
Annotation GO Biobase limma Annotation GO Biobase limma
updated 15.2 years ago by ▴ 810 • written 15.2 years ago by ▴ 830
2
votes
3
replies
1.9k
views
Suppress messages from ALL calls to load package
suppressPackageStartupMessages Biobase
updated 2.4 years ago by ★ 4.0k • written 2.4 years ago by ▴ 210
0
votes
6
replies
1.9k
views
iFlow/flowCore installation problem
Biobase flowCore iFlow Biobase flowCore iFlow
updated 13.1 years ago by ★ 8.2k • written 13.1 years ago by ▴ 60
0
votes
4
replies
1.9k
views
Failure to load Biobase
Biobase affy limma gcrma matchprobes affyio Biobase affy limma gcrma matchprobes affyio
updated 17.9 years ago by 25k • written 17.9 years ago by ★ 2.2k
3
votes
3
replies
1.8k
views
Is there a way to save and open an expression set?
biobase
updated 4.5 years ago by ★ 3.9k • written 4.5 years ago by ▴ 20
0
votes
5
replies
1.8k
views
RMA and justRMA error
Cancer cdf Biobase affy gcrma affyio Cancer cdf Biobase affy gcrma affyio
17.7 years ago Aedin Culhane ▴ 510
0
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 16.9 years ago by ★ 7.4k • written 16.9 years ago by ★ 2.2k
0
votes
1
reply
1.8k
views
Coercing matrix into expression set, for normalization of only subsets of miRNAs (affy miRNA3.0)
miRNA Normalization GO Biobase affy convert oligo miRNA Normalization GO Biobase affy
updated 10.5 years ago by ▴ 190 • written 10.5 years ago by 65k
0
votes
1
reply
1.8k
views
GEOquery, GSEMatrix parameter and lifecycle of GEO series data
GO Biobase PROcess GEOquery GO Biobase PROcess GEOquery
updated 11.8 years ago by 21k • written 11.8 years ago by ▴ 440
2
votes
10
replies
1.8k
views
Am I on the right tracks with a 3 factor design in Limma?
r limma design matrix biobase
updated 5.8 years ago by 50k • written 5.8 years ago by • 0
0
votes
11
replies
1.7k
views
'recursive default argument' error in GOENTREZID2GO
GO Biobase genefilter graph Category GO Biobase genefilter graph Category
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 260
0
votes
4
replies
1.7k
views
[R-SIG-Mac] Mac os x graphviz-Rgraphviz problem
Biobase annotate geneplotter graph Rgraphviz BUS Biobase annotate geneplotter graph BUS
updated 17.2 years ago by ★ 7.4k • written 17.2 years ago by ★ 6.5k
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Problem for loading Bioconductor package in R by touchstoneeduseo • 0
Touchstone is your gateway to English language proficiency! Our institute offers tailored courses designed to prepare students for success …
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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