[BioC] regarding package ArrayExpress

[Misha Kapushesky]

Hi,

Without tweaking read.table, you'd have to read row names as one of the 
data columns, then make.names on that set of names and set the row names 
to the modified ones. So, something like

d <- read.table("foo.tab") ## if read.table("foo.tab", row.names=1) fails

rownames(d) <- make.names(d[,1], unique=TRUE)

d <- d[,-1]                ## to remove the column used

Whether these newly made "unique" row names are what you need is a good 
question... :)

--Misha

On Thu, 10 Sep 2009, audrey at ebi.ac.uk wrote:

> 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
>>
>> 	[[alternative HTML version deleted]]
>>
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