[BioC] Basic questions

[Kasper Daniel Hansen]

On Mar 18, 2008, at 7:49 PM, Chintanu wrote:

> 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'

Given your example below my guess is that in the targets file you call  
your files say
   B1a
where it should be
   B1a.gpr

We probably need to see the contents of the target file if this  
doesn't help.

Kasper


>
>
>> 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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>
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