@@ -522,3 +522,11 @@ function (which expects ff objects and supports parallel processing)

 2010-05-25 R. Scharpf committed version 1.7.2

 ** added example dataset

 ** fixed vignette: inst/scripts/copynumber.Rnw

+

+2010-05-25 R. Scharpf committed version 1.7.3

+** put back in the following check in readIDAT (from r 45050):

+  if(versionNumber<3)

+    stop("Older style IDAT files not supported:  consider updating your scanner settings")

+

+2010-05-25 R. Scharpf committed version 1.7.4

+** wrapped readIDAT in a tryCatch()	   

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.7.3

+Version: 1.7.4

 Date: 2010-05-25

 Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>

 Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -63,6 +63,7 @@ export(crlmm,

 ##       ellipse, 

        genotype, 

        readIdatFiles, 

+       readIdatFiles2,

        snprma,

        snprma2,

        crlmm2,

@@ -87,7 +87,8 @@ readIdatFiles <- function(sampleSheet=NULL,

 	       cat("reading", arrayNames[i], "\t")

 	       idsG = idsR = G = R = NULL

 	       cat(paste(sep, fileExt$green, sep=""), "\t")

-	       G = readIDAT(grnidats[i])

+	       err <- tryCatch(G = readIDAT(grnidats[i]), error=function(e) NULL)

+	       if(is.null(err)) next()

 	       idsG = rownames(G$Quants)

 	       headerInfo$nProbes[i] = G$nSNPsRead

 	       headerInfo$Barcode[i] = G$Barcode

@@ -235,11 +236,11 @@ readIdatFiles2 <- function(sampleSheet=NULL,

 	       stop("Cannot find .idat files")

        if(length(grnfiles)!=length(redfiles))

 	       stop("Cannot find matching .idat files")

-       if(path[1] != "."){

+       if(path[1] != "." & path[1] != ""){

 	       grnidats = file.path(path, grnfiles)

 	       redidats = file.path(path, redfiles)

        }  else {

-	       message("path arg not set.  Assuming files are in local directory")

+	       message("path arg not set.  Assuming files are in local directory, or that complete path is provided")

 	       grnidats <- grnfiles

 	       redidats <- redfiles

        }

@@ -257,11 +258,12 @@ readIdatFiles2 <- function(sampleSheet=NULL,

        dates = list(decode=rep(NA, narrays),

                     scan=rep(NA, narrays))

        ## read in the data

-       for(i in seq(along=arrayNames)) {

+       for(i in seq_along(arrayNames)) {

 	       cat("reading", arrayNames[i], "\t")

 	       idsG = idsR = G = R = NULL

 	       cat(paste(sep, fileExt$green, sep=""), "\t")

-	       G = readIDAT(grnidats[i])

+	       G <- tryCatch(readIDAT(grnidats[i]), error=function(e) NULL)

+	       if(is.null(G)) { cat("\n"); next() }

 	       idsG = rownames(G$Quants)

 	       headerInfo$nProbes[i] = G$nSNPsRead

 	       headerInfo$Barcode[i] = G$Barcode