[BioC] Array express looking in wrong place for file...

[Audrey Kauffmann]

Hi Paul,

I apologize for the delay in replying.

The ArrayExpress database has been completely regenerated two weeks ago 
and some changes (like the naming of the zip files) needed some time to 
get synchronized with the Bioconductor package (especially because I was 
away at the same moment).
The problem of the file names is solved in ArrayExpress version 1.5.11 
and future versions.

If you update the package (using the development version or use the new 
release when it is available), it should work fine.

Please note that for this particular dataset, you will need first to 
download the data using getAE() function and then set the column names 
in the function magetab2bioc() as the scanner column names are 
apparently not part of the known quantitation types from ArrayExpress:

library("ArrayExpress")
EUCON1 = getAE("E-UCON-1")
mRnaData = magetab2bioc(EUCON1, rawcol = list(R="Feature Extraction 
Software:rMeanSignal", G="Feature Extraction Software:gMeanSignal", 
Rb="Feature Extraction Software:rBGMeanSignal", Gb="Feature Extraction 
Software:gBGMeanSignal" ))

Sorry again for the problem and the delay replying,
Audrey

Paul Geeleher wrote:
> Hi I'm getting this error when I try to dowload from ArrayExpress:
>
> mRnaData <- ArrayExpress("E-UCON-1")
> ...
> In getAE(input, path, type = "raw") :
> http://www.ebi.ac.uk/microarray-as/ae/files/E-UCON-1/E-UCON-1.raw.zip  does
> not exist or is empty.
> ...
>
> The thing is its looking in the wrong place for this file, if I go to the
> array express website the files does exist but is at:
>
> http://www.ebi.ac.uk/microarray-as/ae/files/E-UCON-1/E-UCON-1.raw.1.zip
>
> Note the 1 after the word raw...
>
> Any way to specify this address manually? Or another solution? I haven't
> been able to find one.
>
> Thanks alot
>
> -Paul.
>
>
>   

-- 
Audrey Kauffmann
EMBL - EBI
Cambridge UK
+44 (0) 1223 492 631 
http://www.ebi.ac.uk/~audrey