[BioC] Mouse diversity array --building the required files for aroma.affymetrix UGP, UFL

[Ivanek, Robert]

Dear Sir or Madam,

I would like to analyse the copy number variation data from Affymetrix
Mouse Diversity Array. I have not found any information on your website
about this particular array. I have tried to build the annotation files
which are required by aroma but without success. I have few questions
regarding that:

1: Is aroma.affymetrix able to analyse the "Mouse Diversity Array" ?

2: I tried to build the "UGP" file directly from NetAffx annotation
files using the code on your website, however I am getting the following
error.

##
library("aroma.affymetrix")
##                                                                                                                                                           
## create UGP from NetAffx files
cdf <- AffymetrixCdfFile$byChipType("MOUSEDIVm520650")
##
## Creates an empty UGP file for the CDF, if missing.
ugp <- AromaUgpFile$allocateFromCdf(cdf, tags=c("na30", "RI20100526"))
##
## Import NetAffx unit position data
csv <- AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650",
otags=".na30")

Error in list(`AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650",
tags = ".na30")` = <environment>,  :

[2010-05-26 15:11:00] Exception: File format error of the tabular file
('annotationData/chipTypes/MOUSEDIVm520650/NetAffx/MOUSEDIVm520650.na30.annot.csv'): \
line 1 did not have 12 elements
  at throw(Exception(...))
  at throw.default("File format error of the tabular file ('",
getPathname(this), "'): ", ex$message)
  at throw("File format error of the tabular file ('",
getPathname(this), "'): ", ex$message)
  at value[[3]](cond)
  at tryCatchOne(expr, names, parentenv, handlers[[1]])
  at tryCatchList(expr, classes, parentenv, handlers)
  at tryCatch({
  at verify.TabularTextFile(this, ...)
  at verify(this, ...)
  at this(...)
  at newInstance.Class(clazz, ...)
  at newInstance(clazz, ...)
  at newInstance.Object(static, pathname)
  at newInstance(static, pathname)
  at method(static, ...)
  at AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", tags =
".na30")
In addition: Warning message:
In read.table(3L, header = TRUE, colClasses = c(NA_character_,
NA_character_,  :
  not all columns named in 'colClasses' exist


3. I tried it also by using the "manual" approach using the
tab=delimited file, however it seems to me that the mitochondria probes
are skipped  (NA values in ugp[,1] but valid values in ugp[,2]). Another
problem is that some positions for other chromosomes are not loaded in
properly (valid values in ugp[,1] but NA values in ugp[,2]).


Here is the sessionInfo:

R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C
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] aroma.affymetrix_1.6.0 aroma.apd_0.1.7        affxparser_1.20.0
R.huge_0.2.0           aroma.core_1.6.0       aroma.light_1.16.0
 [7] matrixStats_0.2.1      R.rsp_0.3.6            R.cache_0.3.0
R.filesets_0.8.1       digest_0.4.2           R.utils_1.4.0
[13] R.oo_1.7.2             R.methodsS3_1.2.0      RColorBrewer_1.0-2

loaded via a namespace (and not attached):
[1] tools_2.11.0



Best Regards

Robert





-- 
Robert Ivanek
Postdoctoral Fellow Schuebeler Group
Friedrich Miescher Institute
Maulbeerstrasse 66
4058 Basel / Switzerland
Office phone: +41 61 697 6100