[BioC] Problems loading microarray data into Bioconductor

[Jean Yee Hwa Yang]

Hi Craig,

Send me a copy of your gpr file off-line and I will take a look at it for
you.

Jean

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Jean Yee Hwa Yang			 jean at biostat.ucsf.edu
 Lung Biology Center, 		           Tel: (415) 476-3368
 University of California,		   Fax: (415) 476-6014
 500 Parnassus Avenue, MU 420-W,  San Francisco, CA 94143-0560
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Wed, 17 Mar 2004, McKinstry, Craig A wrote:

> Hello 
> 
> I have recently began working with microarray gene expression data and
> am new to this type of analysis. I have been trying to load data from a
> .gpr file and a .gal file in my working directory into an object of
> marrayClass but have been encountering error messages. I run these 3
> lines:
> 
> library(marrayTools)
> library(marrayPlots)
> data <- gpTools(raw=TRUE)
> > data <- gpTools(raw=TRUE)
> [1] NA
> [1] "Reading ./Sr90 5K A total norm 10%.gpr"
> Error in readLines(con, n, ok) : invalid value for `n'
> 
> Investigating this further, I have found that the .gpr files I am using
> have the following lines in the heading section:
> 
> "Type=GenePix Results 1.3"	Suggesting an earlier version of
> "GenePix Results" than is currently supported(?). Example .gpr files I
> have looked at have "Type=GenePix Results 3". 
> 
> Also, I have the line in my .gpr file 
> "Creator=ScanArray Express, Microarray Analysis System 2.1.0.0" which
> varies from the example .gpr files which have the line:
> "Creator=GenePix 4.1.1.4"
> I am not even sure this is the source of the errors I am getting but am
> stymied as to where else to look. Any advice?
> Thanks in advance,
> 
> > Craig A. McKinstry
> > Statistics and Quantitative Sciences
> > Battelle/PNNL
> > 902 Battelle Blvd
> > P.O. Box 999, MSIN K5-12
> > Richland, Washington 99352
> > Phone: (509) 375-6470 or 
> > 	  (509) 376-5611
> > Fax (509) 375-2604
> > Email: craig.mckinstry at pnl.gov
> > http://www.pnl.gov/statistics
> > 
> > 
> 
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