[BioC] ArrayExpress package error

[Audrey Kauffmann]

Dear Srini,

The experiment you are using seems to present two difficulties for the 
automated building of an R object:
- several array designs are used, so instead of one object you will have 
a list containing several sub-objects, each of them corresponding one 
array design.
- the column names used in the raw files are not standard so they are 
not automatically recognised. This is the reason why the error message 
gives you the opportunity to set the argument.

The help page for the function ArrayExpress and the vignette give more 
details on such cases and how to set rawcol.

In this particular case, you can try:
rawset = ArrayExpress("E-SMDB-3834", rawcol = list(G="GenePix:F532 
Mean",R="GenePix:F635 Mean",Gb="GenePix:B532 Median" ,Rb="GenePix:B635 
Median" ))

This will create a list of 4 NChannelSet.

Audrey

Srinivas Iyyer wrote:
> Dear Group,
>
> I have been trying to create rawset using ArrayExpress for the following array dataset. I have error when I ran the following. Any thoughts if error is with the compiled data or functions. thank you. srini
> (sessionInfo - given below)
>   
>> rawset = ArrayExpress("E-SMDB-3834")
>>     
> trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/SMDB/E-SMDB-3834/E-SMDB-3834.raw.zip'
> ftp data connection made, file length 202912584 bytes
> opened URL
> downloaded 193.5 Mb
>
> ###............................... (truncated ) (error apeared after this)
> Read 60 items
> Error in nonAB(i, files, path, ph, rawcol, adr, adf, idf) : 
>   3 scanner names are given ( "GenePix" "SMD" "ScanAlyze" ). It is not possible to handle such a case. Try to set the argument 'rawcol' by choosing among the following columns names: 
> "GenePix:F532 Mean" 
> "GenePix:F635 Mean" 
> ........... (continued...)
>
> In addition: Warning messages:
> 1: In download.file(featureannot, adffile, mode = "wb") :
>   only first element of 'url' argument used
> 2: In download.file(featureannot, adffile, mode = "wb") :
>   only first element of 'destfile' argument used
> Read 61 items
> Error in nonAB(i, files, path, ph, rawcol, adr, adf, idf) : 
>   3 scanner names are given ( "GenePix" "SMD" "ScanAlyze" ). It is not possible to handle such a case. Try to set the argument 'rawcol' by choosing among the following columns names: 
> "GenePix:F532 Mean" 
> "GenePix:F635 Mean" 
>
> Read 42 items
> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "experimentData", for signature "list"
>
>
>
>
>   
>> sessionInfo()
>>     
> R version 2.8.0 (2008-10-20) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] ArrayExpress_1.2.2 XML_1.98-1         limma_2.16.2       affy_1.20.0        Biobase_2.2.1     
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        preprocessCore_1.4.0
>
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>   

-- 
Audrey Kauffmann
EMBL - EBI
Cambridge UK
http://www.ebi.ac.uk/~audrey