Hi,
I'm runing some QC analysis with 5 Affy mouse genechip HT430PM
I've installed the required libraries(affy, arrayQualityMetrics,
htmg430pmcdf) and all dependecies
I'm using the following code:
fls <- list.files("/", ".*CEL")
eset <- justRMA(filenames = fls)
aBatch <- ReadAffy(filenames = fls)
arrayQualityMetrics(aBatch,outdir = "report")

The last commad shows the following error message:

The report will be written in directory 'report'.
Error in setQCEnvironment(cdfn) :
  Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy
does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC parameters
manually.

Error in density.default(as.matrix(log2(mm(expressionset))), ...) :
  'x' contains missing values
In addition: Warning message:
In aqm.qcstats(expressionset) :
  'plot(qcStats)' from the package 'simpleaffy' failed for this dataset.
Error in obj[[i]]$legend : $ operator is invalid for atomic vectors
In addition: Warning message:
In arrayQualityMetrics(aBatch, outdir = "report") :
  Cannot draw the Perfect Match versus MisMatch plot

Any idea about the orgin of this error ?
Thanks in advance for your help.
Kind regards
Ramzi
----------------------------------------------------------------

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0
[3] preprocessCore_1.8.0      gcrma_2.18.0
[5] htmg430pmcdf_2.5.0        affy_1.24.2
[7] Biobase_2.6.1
loaded via a namespace (and not attached):
 [1] affyio_1.14.0       annotate_1.24.0     AnnotationDbi_1.8.1
 [4] beadarray_1.14.0    Biostrings_2.14.8   DBI_0.2-4
 [7] genefilter_1.28.2   grid_2.10.1         hwriter_1.1
[10] IRanges_1.4.9       lattice_0.17-26     latticeExtra_0.6-4
[13] limma_3.2.1         marray_1.24.0       RColorBrewer_1.0-2
[16] RSQLite_0.7-3       simpleaffy_2.22.0   splines_2.10.1
[19] stats4_2.10.1       survival_2.35-8     tcltk_2.10.1
[22] tools_2.10.1        vsn_3.14.0          xtable_1.5-6

	[[alternative HTML version deleted]]

