[BioC] Questions on arrayQuality

Paquet, Agnes apaquet at medsfgh.ucsf.edu
Thu Jul 8 01:45:55 CEST 2004

Dear Richard,

We have been modifying several things in arrayQuality package since the
release. The latest version of the package is available from our website
http://arrays.ucsf.edu/software. In particular, the problem with the missing
images in the manual should be fixed. 

You can install it by typing in R:

For Spot output:

arrayQuality is not reading output from Spot directly at the moment. You can
still generate diagnostic plots from a Spot file by reading your data into a
RGList using the function read.maimage(source="spot") from limma, or into a
marrayRaw object using read.Spot function from marray. Then, call the
function maQualityPlots using your new object as argument.

I am planning to extend the 9mers and QCHyb quality control functions to
Spot files soon.

"2. Is there a way to custom specify the location of the 9-mers?"

I refer to 9-mers oligos as random small oligos that are hybridized to the
array to verify that all spots have been printed properly, not to the actual
probes on the arrays. As I am not sure to understand your question
completely, could you please give me more details about what you would like
to achieve?

3. Acuity
Acuity is a software developed by Axon Instruments that we use as database,
analysis and visualization tool. For more information:



-----Original Message-----
From: Richard Friedman [mailto:friedman at cancercenter.columbia.edu] 
Sent: Wednesday, July 07, 2004 12:16 PM
To: 'Bioconductor Mail List'
Subject: [BioC] Questions on arrayQuality

Dear All,

	I have the following questions on arrayQuality:

1. The documentation for 9-mer hybridizations discusses gpr files
      (the output of GenePix). Can arrayQuality be used for output
      from Spot?
2. Is there a way to custom specify the location of the 9-mers?
3. A program called Acuity is cited. What is Acuity?
4. Several of the figures did not come out with the html file that
     was in the doc folder.
Is a pdf file available?

Thanks and best wishes,
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu

"If Dylan uses the word "the" and Donne
uses the word "the" does he say that
Dylan is making a reference to Donne?"
-Rose Friedman, age 7

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