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@pnl.gov > http://www.pnl.gov/statistics > > [[alternative HTML version deleted]]

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@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@pnl.gov > > http://www.pnl.gov/statistics > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >