On Wednesday 11 April 2007 10:11, Weixiang Liu wrote:
> Dear all,
>
> Is there any R product for convertion from an affymetrix probe to
GO id?
> Or other related code?
Hi, Weixiang. The simplest place to start is with the documentation
for the
annotate package, available at the Bioconductor website. There are
vignettes
(think of them as tutorials) on using the package. Two, in
particular, may
be of immediate use, the "useDataPkgs.pdf" and the "GOusage.pdf".
Sean
Hi Weixiang:
You need to tell us which chip you are using:
I assume you are using hgu133a:
then you need to look at hgu133aGO2PROBE {hgu133a}
You probably also need GO package to convert GO id to its description.
HTH,
Weiwei
On 4/11/07, Weixiang Liu <victorwxliu at="" yahoo.com.cn=""> wrote:
> Dear all,
>
> Is there any R product for convertion from an affymetrix probe to
GO id? Or other related code?
>
> Thanks.
>
> Best wishes
> Weixiang
>
>
> ---------------------------------
> ????????????????-3.5G??????20M??????
> [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
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http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
"Did you always know?"
"No, I did not. But I believed..."
---Matrix III
sorry I misread your post, you are asking form probe to GO, here is
the code using hgu133a as an example:
library(hgu133a)
cc <- as.list(hgu133aGO)
t1 <- sapply(cc, function(x) sapply(x, function(y) y[[1]]))
> t1[1:3]
$`208608_s_at`
GO:0003779 GO:0005509 GO:0005516 GO:0005856 GO:0006936
GO:0016010 GO:0016020
"GO:0003779" "GO:0005509" "GO:0005516" "GO:0005856" "GO:0006936"
"GO:0016010" "GO:0016020"
$`205536_at`
GO:0005089 GO:0005515 GO:0005622 GO:0007242 GO:0008270
GO:0019992 GO:0035023 GO:0046872
"GO:0005089" "GO:0005515" "GO:0005622" "GO:0007242" "GO:0008270"
"GO:0019992" "GO:0035023" "GO:0046872"
$`210256_s_at`
GO:0016020 GO:0016301 GO:0016308 GO:0016740
"GO:0016020" "GO:0016301" "GO:0016308" "GO:0016740"
HTH,
Weiwei
On 4/11/07, Weixiang Liu <victorwxliu at="" yahoo.com.cn=""> wrote:
> Dear all,
>
> Is there any R product for convertion from an affymetrix probe to
GO id? Or other related code?
>
> Thanks.
>
> Best wishes
> Weixiang
>
>
> ---------------------------------
> ????????????????-3.5G??????20M??????
> [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
"Did you always know?"
"No, I did not. But I believed..."
---Matrix III
