In package affy version 1.2.27, there is a mistype error in the code of xy2indices : function (x, y, nr = NULL, cel = NULL, abatch = NULL) { if (any(x <= 0) || any(y <= 0)) stop("Xs and Ys must start at 1 (please refer to the help file) !") /* ***nc*** should be ***nr*** */ ct <- sum(c(is.null(nc), is.null(cel), is.null(abatch))) ^^^ if (ct != 2) /* and here again */ stop("One and only one of 'nc', 'cel', 'abatch' should be specified.") ^^^ if (!is.null(cel)) nr <- nrow(intensity(cel)) if (!is.null((abatch))) nr <- nrow(abatch) return(x + nr * (y - 1)) } Sorry if this is a known/fixed issue. PYBoelle FdM StAntoine PARIS [[alternate HTML version deleted]]

The typo only existed for a short time.. it was fixed before the release... ... strange... http://franz.stat.wisc.edu/cgi-bin/viewcvs.cgi/Rpacks/affy/R/xy2indice s.R?rev=1.3&cvsroot=Bioconductor&content-type=text/vnd.viewcvs-markup note: the typo is the error message is still there. It will be fixed... Thanks, L. On Tue, Jun 10, 2003 at 05:59:46PM +0200, Pierre-yves Bo?lle wrote: > In package affy version 1.2.27, there is a mistype error in the code of xy2indices : > > function (x, y, nr = NULL, cel = NULL, abatch = NULL) > { > if (any(x <= 0) || any(y <= 0)) > stop("Xs and Ys must start at 1 (please refer to the help file) !") > > /* ***nc*** should be ***nr*** */ > ct <- sum(c(is.null(nc), is.null(cel), is.null(abatch))) > ^^^ > > if (ct != 2) > /* and here again */ > stop("One and only one of 'nc', 'cel', 'abatch' should be specified.") > ^^^ > > > if (!is.null(cel)) > nr <- nrow(intensity(cel)) > if (!is.null((abatch))) > nr <- nrow(abatch) > return(x + nr * (y - 1)) > } > > Sorry if this is a known/fixed issue. > > PYBoelle > FdM StAntoine > PARIS > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent