[BioC] regarding package ArrayExpress

[audrey at ebi.ac.uk]

Dear Amit,

You are not making any mistakes. This is the proper way of calling the
functions to create an object from a processed dataset. However the
problem comes from the dataset itself. It contains duplicate probe
identifiers as row names, which is not allowed by the function read.table
that is used in the procset function.
Unfortunately I do not have an idea on how to prevent this. Does someone
know how I could allow duplicate row names in my function?

Best regards,
Audrey

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

> Hello! List,
>
> I am trying to build an object from Array Express processed data using
> bioconductor package ArrayExpress. I did following:-
>
> CAGE99d = getAE("E-GAGE-99",type="processed")
> colname = getcolproc(CAGE99d)
> CAGE99p = procset(CAGE99d, colname[3])
>
> and I got following error:-
> Error in `row.names<-.data.frame`(`*tmp*`, value = c(6995L, 7017L, 7006L,
> :
>
>   duplicate 'row.names' are not allowed
> In addition: Warning message:
> non-unique values when setting 'row.names': ‘R:A-MEXP-58:210099’,
> ‘R:A-MEXP-58:210100’, ‘R:A-MEXP-58:210111’,
> ‘R:A-MEXP-58:210123’,‘R:A-MEXP-
> [... truncated]
>
> I am not able to figure out mistake I am making. Please Help!
> Amit
>
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>
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