[BioC] A couple of questions
Mon, 30 Sep 2002 23:55:31 +0200
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
>directly from my database if possible. Do you have any suggestions as to
>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.
Dr. Wolfgang Huber
Division of Molecular Genome Analysis
[mailto:email@example.com]On Behalf Of Ali Al-Timimi
Sent: Monday, September 30, 2002 9:53 PM
Subject: [BioC] A couple of questions
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
>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
>Ratio ch1 Confidence ch2 Intensity ch2 Background ch2 Intensity
>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?
Center for Biomedical Genomics and Informatics
George Mason University
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