Hi!

I'd like to ask 3-basic questions on Bioconductor:

* Having the target file, gpr and gal file all in the same directory as R,
what the following error message is actually referring to :

> library(arrayQuality)
> TargetInfo <- read.marrayInfo ("targets11.txt")
> mraw <- read.GenePix (targets = TargetInfo)
Error in file(con, "r") : unable to open connection
In addition: Warning message:
In file(con, "r") :
  cannot open file './B1a', reason 'No such file or directory'



> sessionInfo()

R version 2.6.0 (2007-10-03)

i386-pc-mingw32

locale:

LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_MONETARY=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252



attached base packages:

 [1] grid      tools     stats     graphics  grDevices datasets  tcltk
utils     methods   base



other attached packages:

 [1] arrayQuality_1.14.0 RColorBrewer_1.0-2  gridBase_0.4-3
hexbin_1.12.0       lattice_0.17-6      convert_1.14.0
Biobase_1.16.3

 [8] marray_1.16.0       limma_2.12.0        svSocket_0.9-5
svIO_0.9-5          R2HTML_1.58         svMisc_0.9-5        svIDE_0.9-5



*  Again, I'm also getting an Error message with the Gal file [sessionInfo()
is same as above].

> library(arrayQuality)

> targets <- readTargets("targets11.txt")

> RG <- read.maimages(targets$FileName,source="genepix",ext="gpr")
Read B1a.gpr
Read B1b.gpr
Read B1cDS.gpr
> names(RG$genes)
[1] "Block"  "Row"    "Column" "ID"     "Name"

> RG$genes <- readGAL()
Error in readGAL() : Cannot find ID and Name columns in GAL file



*  I have gone through the short description given in LIMMA User's guide, 18
April 2007 (from page 32 onwards) on microarry design matrix. Is there any
other reference(s) one can refer to ?

Thanks for any comment and help,

Chintanu

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