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@@ -533,3 +533,6 @@ function (which expects ff objects and supports parallel processing) |
| 533 | 533 |
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2010-05-26 R. Scharpf committed version 1.7.5 |
| 535 | 535 |
** minor edits to inst/scripts/copynumber.Rnw |
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+ |
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+2010-07-25 M. Ritchie committed version 1.7.6 |
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+** fixed bug introduced in 1.7.4 by addition of tryCatch() into readIdatFiles(). Thanks to Nolwenn Le Meur for pointing this out. |
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@@ -1,8 +1,8 @@ |
| 1 | 1 |
Package: crlmm |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
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-Version: 1.7.5 |
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-Date: 2010-05-25 |
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+Version: 1.7.6 |
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+Date: 2010-07-25 |
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| 6 | 6 |
Author: Rafael A Irizarry, Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au> |
| 7 | 7 |
Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| 8 | 8 |
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms |
| ... | ... |
@@ -87,8 +87,11 @@ readIdatFiles <- function(sampleSheet=NULL, |
| 87 | 87 |
cat("reading", arrayNames[i], "\t")
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| 88 | 88 |
idsG = idsR = G = R = NULL |
| 89 | 89 |
cat(paste(sep, fileExt$green, sep=""), "\t") |
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- err <- tryCatch(G = readIDAT(grnidats[i]), error=function(e) NULL) |
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- if(is.null(err)) next() |
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+ G <- tryCatch(readIDAT(grnidats[i]), error=function(e) NULL) |
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+ if(is.null(G)) {
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+ if(i==1) stop("Read in of first IDAT file failed - check your data")
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+ else cat("\n"); next()
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+ } |
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idsG = rownames(G$Quants) |
| 93 | 96 |
headerInfo$nProbes[i] = G$nSNPsRead |
| 94 | 97 |
headerInfo$Barcode[i] = G$Barcode |
| ... | ... |
@@ -263,7 +266,10 @@ readIdatFiles2 <- function(sampleSheet=NULL, |
| 263 | 266 |
idsG = idsR = G = R = NULL |
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cat(paste(sep, fileExt$green, sep=""), "\t") |
| 265 | 268 |
G <- tryCatch(readIDAT(grnidats[i]), error=function(e) NULL) |
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- if(is.null(G)) { cat("\n"); next() }
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+ if(is.null(G)) {
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+ if(i==1) stop("Read in of first IDAT file failed - check your data")
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+ else cat("\n"); next()
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+ } |
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| 267 | 273 |
idsG = rownames(G$Quants) |
| 268 | 274 |
headerInfo$nProbes[i] = G$nSNPsRead |
| 269 | 275 |
headerInfo$Barcode[i] = G$Barcode |
