[BioC] ArrayExpress error attaching phenodata

[Audrey Kauffmann]

Hi Paul,

I am sorry for the delay replying.
Indeed, usually in the sdrf file there is only one line per array which is
why this particular dataset was causing an error. It has two lines per
array, each line corresponding to a channel.
What you can do is downloading the data using the getAE() function
manually correct the sdrf so that there is only one line per array
(merging the two lines per channel for instance). And then you should be
able to build the object with the corrected sdrf file using the
magetab2bioc() function.
That should do the trick, please let me know if it worked.
I probably need to make some changes to the package to handle such cases
if sdrf file can contain one line per channel for two colour arrays.

Best wishes,
Audrey

> Hi,
>
> I'm running the following command to download an ArrayExpress dataset:
>
> "rawMrnaSet <- ArrayExpress("E-UCON-1", rawcol = list(R="Feature
> Extraction Software:rMeanSignal", G="Feature Extraction
> Software:gMeanSignal", Rb="Feature Extraction Software:rBGMeanSignal",
> Gb="Feature Extraction Software:gBGMeanSignal" ))"
>
> The data downloads and builds the object but I get the following errir
> at the end:
>
> "Cannot attach phenoData to the object as the Array Data File column
> of the sdrf file contains duplicated elements."
>
> The sdrf file is located here:
> http://www.ebi.ac.uk/microarray-as/ae/files/E-UCON-1/E-UCON-1.sdrf.txt
>
> I'm wondering what exactly is wrong with the file and how I can fix
> this? Also note that the sdrf file has 614 rows but there is only 307
> samples, I wonder if this is normal for two-channel data like this and
> if ArrayExpress "knows" what to do with it?
>
> Paul
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
>
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