[BioC] help with SCAN.UPC and u133aaofav2

Steve Piccolo stephen.piccolo at hsc.utah.edu
Fri Nov 1 15:53:59 CET 2013

Hi Juliet,

Thanks for your question.

You can get around this by using the "annotationPackageName" parameter to
indicate an annotation package that describes the layout for these chips.
I don't know of an annotation package specifically for these "early
access" arrays. But from what I can tell, the layout of these chips is
exactly the same as the HT U133A arrays (which superseded the EA arrays).
So what you can do is indicate that you want to use the annotation package
for the HT U133A arrays.

Below is an example:

Normalized = SCAN("myCEL.CEL", annotationPackageName="pd.ht.hg.u133a")

You may need to install this package manually, or Bioconductor may take
care of it for you automatically (I can't remember). The documentation
describes more detail, but please let me know if you run into problems.


Stephen Piccolo, Ph.D.
Postdoctoral Research Associate

  Division of Computational Biomedicine, Boston University School of

  Department of Pharmacology and Toxicology, University of Utah

Twitter: @stevepiccolo

From:  Juliet Hannah <juliet.hannah at gmail.com>
Date:  Thursday, October 31, 2013 7:56 PM
To:  Bioconductor mailing list <bioconductor at r-project.org>, "W. Evan
Johnson" <wej at bu.edu>, Stephen Piccolo <stephen.piccolo at hsc.utah.edu>
Subject:  help with SCAN.UPC and u133aaofav2


I am trying to run scan and I obtain the following error. I searched for
the packages (pd.u133aaofav2), could not find them, and I'm confused about
how to proceed:

# command used

normalized = SCAN("myCEL.CEL")

# error message

Loading required package: pd.u133aaofav2
Attempting to obtain 'pd.u133aaofav2' from BioConductor website.
Checking to see if your internet connection works...
Package 'pd.u133aaofav2' was not found in the BioConductor repository.
The 'pdInfoBuilder' package can often be used in situations like this.
Error in { : 
  task 1 failed - "The annotation package, pd.u133aaofav2, could not be
In addition: Warning messages:
1: executing %dopar% sequentially: no parallel backend registered
2: In library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE,  :
  there is no package called âpd.u133aaofav2â

# sessionInfo()

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base     

other attached packages:
 [1] SCAN.UPC_2.4.0      foreach_1.4.1       affyio_1.30.0
 [4] affy_1.40.0         GEOquery_2.28.0     Biostrings_2.30.0
 [7] XVector_0.2.0       IRanges_1.20.4      oligo_1.26.0
[10] oligoClasses_1.24.0 Biobase_2.22.0      BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] affxparser_1.34.0     BiocInstaller_1.12.0  bit_1.1-10
 [4] codetools_0.2-8       compiler_3.0.2        DBI_0.2-7
 [7] ff_2.2-12             GenomicRanges_1.14.3  iterators_1.0.6
[10] MASS_7.3-29           preprocessCore_1.24.0 RCurl_1.95-4.1
[13] splines_3.0.2         stats4_3.0.2          tools_3.0.2
[16] XML_3.98-1.1          zlibbioc_1.8.0    

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