Hi everyone! I am quite new to Bioconductor project. Is there a possibility to read and manipulate DAT files that come from Affymetrix? I tried to read it as simple .dat file, but instead of reading the image R brings this line to me: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got '�}}' I guess this is not a normal DAT file, so if anybody has any information on how can I play with affymetrix dat files, let me know. Thank you in advance! Alex [[alternative HTML version deleted]]

Hi Alex, On 6/9/2011 6:37 AM, Aleksandra .. wrote: > Hi everyone! > > I am quite new to Bioconductor project. Is there a possibility to read and > manipulate DAT files that come from Affymetrix? I tried to read it as simple > .dat file, but instead of reading the image R brings this line to me: > > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > scan() expected 'a real', got '???}}' > > I guess this is not a normal DAT file, so if anybody has any That _is_ a normal DAT file. They have been binary format for years now, so you will not be able to read in as if they are simple text files. > information on how can I play with affymetrix dat files, let me know. I don't think there are packages that are designed explicitly to work directly with DAT files. In addition, you would have to get the file that Affymetrix uses to grid the individual pixels into probe regions, and I have never seen that file used outside of Affy's own products. The first place to look would be the Affymetrix SDK to see if they even expose functions for working with DAT files. Then you could either modify the affxparser package to use those functions (if they exist), or plead mightily with Kaspar, Henrik or James to see if they would add them. Best, Jim > > Thank you in advance! > > Alex > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues