Hi Juliet,

For the SCAN paper, we used the Python version of the SCAN code. Since that time, I ported everything to R/Bioconductor. I have a colleague who recently needed to analyze u133aaofav2 arrays from CMAP, and the approach I described worked well for him with the Bioconductor version of SCAN.

Thanks,
-Steve

From: Juliet Hannah <juliet.hannah@gmail.com<mailto:juliet.hannah@gmail.com>>
Date: Friday, November 1, 2013 9:42 AM
To: Stephen Piccolo <stephen.piccolo@hsc.utah.edu<mailto:stephen.piccolo@hsc.utah.edu>>
Cc: Bioconductor mailing list <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>
Subject: Re: help with SCAN.UPC and u133aaofav2

Hi Steve,

Thanks for responding.

I am using the cmap data, which I believe was used in your SCAN paper. Did you you the three types of chips?

Thanks,

Juliet


On Fri, Nov 1, 2013 at 10:53 AM, Steve Piccolo <stephen.piccolo@hsc.utah.edu<mailto:stephen.piccolo@hsc.utah.edu>> wrote:
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exactly the same as the HT U133A arrays (which superseded the EA arrays).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.

Regards,
-Steve

---------------------------------------------------------------------------
---------------
Stephen Piccolo, Ph.D.
Postdoctoral Research Associate

Affiliations:
  Division of Computational Biomedicine, Boston University School of
Medicine

  Department of Pharmacology and Toxicology, University of Utah

Twitter: @stevepiccolo
---------------------------------------------------------------------------
----------------------------







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


All,

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
loaded."
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 āpd.u133aaofav2ā



# sessionInfo()

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

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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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