[BioC] make.cdf.package Error in copySubstitute

[James W. MacDonald]

Hi Matthew,

You cannot use the makecdfenv/affy analysis pipeline for this array.

You can use pdInfoBuilder/oligo, and presumably xps (although Christian 
Stratowa will know for sure about that). Note that the infrastructure 
for pdInfoBuilder and oligo have recently been added, so you will need 
to use R-devel to get the functionality. Also see this:

https://stat.ethz.ch/pipermail/bioconductor/attachments/20140208/f885a15d/attachment.pl

And note that there are no (to my knowledge) HTA specific analysis 
packages in BioC, so if you want to do something similar to what Affy's 
TAC software does, you will have to roll your own.

Best,

Jim


On 3/25/2014 7:06 PM, matthew vitalone wrote:
> Hi,
>
> I am trying to create a cdf package to analyise a set of Affy HTA2.0
> arrays, which don't have one yet. I have followed the documentation, but I
> get this message:
>
> Creating package in C:/Matthew/Sen vs. non-Sen/HTA
> data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir,
> full.names = TRUE), pkgdir, symbolValues,  :
>    'symbolValues' must only contain characters.
>
> I'm not sure where to go next. I'm not sure how to fix this as this
> function is called by biobase, which is called by make.cdf.package
> function. All I need is this package to move forward in the analysis.
>
> Here are the details of my session. R3.0.2 in RStudio
>
>
>
> ##################
>
> library(limma)library(gcrma)
>
>
> Loading required package: affy Loading required package: BiocGenerics Loading
> required package: parallel Attaching package: 'BiocGenerics' The following
> objects are masked from 'package:parallel': clusterApply, clusterApplyLB,
> clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
> parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following
> object is masked from 'package:limma': plotMA The following object is
> masked from 'package:stats': xtabs The following objects are masked from
> 'package:base': anyDuplicated, append, as.data.frame, as.vector, cbind,
> colnames, duplicated, eval, evalq, Filter, Find, get, intersect,
> is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply,
> setdiff, sort, table, tapply, union, unique, unlist Loading required
> package: Biobase Welcome to Bioconductor Vignettes contain introductory
> material; view with 'browseVignettes()'. To cite Bioconductor, see
> 'citation("Biobase")', and for packages 'citation("pkgname")'. >
> setwd("C:/Matthew/Sen
> vs. non-Sen/HTA data") > targets <- readTargets("targets.txt") > View(targets)
>> ab <- ReadAffy(filenames=targets$FileName) > eset <- gcrma(ab) Error in
> getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered: Specified environment does not contain HTA-2_0 Library -
> package hta20cdf not installed Bioconductor - hta20cdf not available
>
>
>
> ##Trying to create cdf package
> ## Contacted Affymetrix and downloaded their CDF file for these arrays
>
> source("http://bioconductor.org/biocLite.R")Bioconductor version 2.13
> (BiocInstaller 1.12.0), ?biocLite for
> helpbiocLite("makecdfenv")BioC_mirror: http://bioconductor.orgUsing
> Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
> 3.0.2.Installing package(s) 'makecdfenv'trying URL
> 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/makecdfenv_1.38.0.zip'Content
> type 'application/zip' length 3373763 bytes (3.2 Mb)opened
> URLdownloaded 3.2 Mb
> package 'makecdfenv' successfully unpacked and MD5 sums checked
>
>
>
> make.cdf.package("HTA-2_0.r1.Psrs_mps.cdf",+
> packagename = "HTA-2_0.r1.Psrs_mps",+                  cdf.path =
> getwd(),+                  package.path = getwd(),+
> compress = FALSE,+                  author = "The Bioconductor
> Project",+                  maintainer = "Biocore Data Team
> <biocannotation at lists.fhcrc.org>",+                  version =
> packageDescription("makecdfenv", fields ="1.0"),+
> species = "Homo_sapiens",+                  unlink = TRUE,+
>        verbose = TRUE)Reading CDF file.
> Creating CDF environment
> Wait for about 681
> dots..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> Creating package in C:/Matthew/Sen vs. non-Sen/HTA
> data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir,
> full.names = TRUE), pkgdir, symbolValues,  :
>    'symbolValues' must only contain characters.
>
>
> Thanks,
> Matthew
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099