[BioC] Problems loading microarray data into Bioconductor

McKinstry, Craig A Craig.Mckinstry at pnl.gov
Wed Mar 17 18:55:22 MET 2004


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

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" which
varies from the example .gpr files which have the line:
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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