[BioC] MOE430 A and B

[Aedin]

Hi
I am having problems using annaffy GO (aafGO) annotations on these chips? I
have updated my chip annotation files, and GO library, but still get

> a<-aafGO(rownames(chipA), "moe430a")
Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found

Thanks for your help,
Aedin

-----Original Message-----
From: bioconductor-bounces+aedin.culhane=ucd.ie at stat.math.ethz.ch
[mailto:bioconductor-bounces+aedin.culhane=ucd.ie at stat.math.ethz.ch]On
Behalf Of Ben Bolstad
Sent: 15 March 2004 14:17
To: peter robinson
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] MOE430 A and B


you need to read in the type A and type B files into separate affybatch
objects.

eg

my.Data.A <-
ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel"))

my.Data.B <-
ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel"))

Ben






On Mon, 2004-03-15 at 04:20, peter robinson wrote:
> Dear List members,
>
> I would like to use the affy package to analyze data from MOE430A and -B
> chips. I tried to read in data from both types of chips at once using
> data <- ReadAffy(widget=T)
> and then reading in 3 MOE430A and 3 MOE430B CEL files.
> I got the error message:
> "Cel file does not seem to beo of 430MOEA type" when the script tried to
input
> data from a 430MOEB Cel file. I had imported the CDF and annotation
packages
> for both types of chip.
> I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system.
>
> Thanks for any advice/tips!
>
> Peter
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
--
Ben Bolstad <bolstad at stat.berkeley.edu>
http://www.stat.berkeley.edu/~bolstad

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