[BioC] pd.hg18.60mer.expr_1.1.1 and Nimblegen data for oligo package in R

[JEAN-YVES SGRO]

Madison 20 June 2008

In order to test the "oligo" package I have tried to follow the R method in the following document by Benilton Carvalho

http://www.bioconductor.org/workshops/2007/BioC2007/labs/oligo/BioC2007-oligo.pdf

After many attempts it is time to write.

First of, Nimblegen does not by default provide the XYS file, but they can be special-ordered (as I found from others postings). 

Even with the test-run data called extdata from library(maqcExpression4plex) there is still something missing and that's the package pd.hg18.60mer.expr_1.1.1 as shown in the error:


>   maqc <- read.xysfiles(xys.files)
Loading required package: pd.hg18.60mer.expr
Error in read.xysfiles(xys.files) : 
  Must install the pd.hg18.60mer.expr package.
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pd.hg18.60mer.expr'
>

I obtain the same error if I try to load other XYS files from another source:

> DATA <- read.xysfiles(xys.files)
Loading required package: pd.hg18.60mer.expr
Error in read.xysfiles(xys.files) : 
  Must install the pd.hg18.60mer.expr package.


Searching with Google, the only document that ever mention this package is the PDF file of the tutorial (in the last slide after the > sessionInfo() command....

I looked within the Bioconductor lists of 2.3, 2.2, 2.1., 2.0, 1.9 at which point there is no more package starting with pd.xxx

I also did a search on Nimblegen analysis in Google and essentially did not find anything else useful for R.

My question is this: is this package available "somewhere?" but from Google results on pd.hg18.60mer.expr_1.1.1, pd.hg18.60mer.expr and pd.hg18.60mer the ONLY document that has this string of character is the PDF tutorial...

A corollary question: is there a way to do a similar analysis without the XYS file using the .pair or other standard files provided by Nimblegen?

Thank you for any hint you might provide... perhaps I am not the only one wondering!

Jean-Yves Sgro

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Jean-Yves Sgro, Ph.D., Senior Scientist
http://myprofile.cos.com/sgroj65
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University of Wisconsin 
Biotechnology Center Gene Expression Center
425 Henry Mall Madison Wi 53706 USA
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& Institute for Molecular Virology
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P.S. Here is the sessionInfo() from the Windows version I have tried to do this in: after the following library commands from http://www.bioconductor.org/workshops/2007/BioC2007/labs/oligo/BioC2007-oligo.R

  library(oligo)
  library(maqcExpression4plex)
  library(genefilter)
  library(geneplotter)
  library(limma)
  library(RColorBrewer)
  palette(brewer.pal(8, "Dark2"))


> sessionInfo()
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] maqcExpression4plex_1.2 oligo_1.4.0             oligoClasses_1.2.0      affxparser_1.12.2      
 [5] preprocessCore_1.2.0    RColorBrewer_1.0-2      limma_2.14.4            geneplotter_1.18.0     
 [9] annotate_1.18.0         xtable_1.5-2            AnnotationDbi_1.2.1     RSQLite_0.6-8          
[13] DBI_0.2-4               lattice_0.17-6          genefilter_1.20.0       survival_2.34-1        
[17] Biobase_2.0.1          

loaded via a namespace (and not attached):
[1] grid_2.7.0         KernSmooth_2.22-22
>