[BioC] limma and ArrayVision

[Gordon K Smyth]

> Hi all!
>
> I tried to use read.maimages to read ArrayVision files as Gordon
> suggested. Unfortunately I get the following:
>
>  > read.maimages("12371987B.csv", source="arrayvision", sep=",")
> Error in match.arg(source, c("spot", "spot.close.open", "genepix",
> "quantarray")) :
>          ARG should be one of spot, spot.close.open, genepix, quantarray
>  >
>
> I've just updated all the packages so I think this is not the problem.

Yes it is the problem.  The message that you quote is from limma version
1.0.8, i.e., the last official BioC release, rather than from limma 1.2.4
which is the most recent development version.  You have apparently
"updated all the packages" simply by re-installing the last official
release of the packages.  If you want newer versions of the packages, you
have to install the development versions of the packages.

Gordon

> Have you any suggestion?
>
> Thank you a lot in advance,
> best
> Alessandro
>
>
>
> At 23.43 28/08/03 +1000, you wrote:
>>Thanks to help from Isaac Mehl, limma now supports ArrayVision data.
>> The support is in limma 1.1.12.
>>
>>The data file attached by Isaac is read by
>>
>>   read.maimages("12371987B.csv", source="arrayvision", sep=",")
>>
>>Cheers
>>Gordon