[BioC] A couple of questions

[Wolfgang Huber]

Hi Ali,

with regards to reading data from QuantArray, you can always use the R
functions read.table or read.delim (type "help(read.delim)" at the R prompt)
and then later call the constructors e.g. for marrayRaw with the appropriate
matrices. However, Sandrine Dudoit would know much better about this!

>My second question is I would like to have the classes you have created
read
>directly from my database if possible. Do you have any suggestions as to
how
>that can be approached?
Check out the DBI: R/Splus Database Interface
at http://cran.r-project.org/ -> Package Sources.
or the various DBMS-specific packages.

Best regards
Wolfgang

Dr. Wolfgang Huber
http://www.dkfz.de/abt0840/whuber
Tel +49-6221-424709
Fax +49-6221-42524709
DKFZ
Division of Molecular Genome Analysis
69120 Heidelberg
Germany

-----Original Message-----
From: bioconductor-admin@stat.math.ethz.ch
[mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Ali Al-Timimi
Sent: Monday, September 30, 2002 9:53 PM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] A couple of questions


Hello everyone,

I would like to first to thank you all for providing such a great service.
I've download the code base and played around with it, but I have a couple
of straightforward questions.

I am trying to load my own data but I am unsure as to what format(s) I
should place it in. I have 2-colored cDNA and I have seen the swirl data you
have provided but I am not certain if I have to map my data to that format.
Here at George Mason University, we use QuantArray so our data comes out
with the following format:

>Number    Array Row    Array Column    Row    Column    Name    X Location
Y
>Location    ch1 Intensity    ch1 Background    ch1 Intensity Std Dev    ch1
>Background Std Dev    ch1 Diameter    ch1 Area    ch1 Footprint    ch1
>Circularity    ch1 Spot Uniformity    ch1 Bkg. Uniformity    ch1 Signal
Noise
>Ratio    ch1 Confidence    ch2 Intensity    ch2 Background    ch2 Intensity
Std
>Dev    ch2 Background Std Dev    ch2 Diameter    ch2 Area    ch2 Footprint
>ch2 Circularity    ch2 Spot Uniformity    ch2 Bkg. Uniformity    ch2 Signal
>Noise Ratio    ch2 Confidence    Ignore Filter

My second question is I would like to have the classes you have created read
directly from my database if possible. Do you have any suggestions as to how
that can be approached?

Sincerely,

Ali Al-Timimi
Graduate Student
Center for Biomedical Genomics and Informatics
George Mason University


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