[BioC] Extract top-ranked genes from model fit

[Claus-Jürgen Scholz]

Hi Chintanu,

why don't you try it with biomaRt using the following code:

library(biomaRt)

# connect to biomaRt server
hs.ensembl <- useDataset("hsapiens_gene_ensembl",useMart("ensembl"))

# retrieve ID information
my.id.list <-
getBM(attributes=c("unigene","affy_hg_u133a"),filters="affy_hg_u133a",values=test_results[,1],mart=hs.ensembl)

# remove empty unigene IDs
my.sub.list <- subset(my.id.list,unigene!="")

# attach unigene IDs
index <- match(test_results[,1],my.sub.list$affy_hg_u133a)
annotated.test_results <- cbind(test_results,my.sub.list$unigene[index])


I hope that helps...

Cheers,
CJ


Chintanu schrieb:
> Hi,
>
> I wish to get the UniGene annotation of the top ranked genes for two sets of
> Affymetrix files (Diseased vs. Reference; chip type: hgu133a). I am
> uncertain as to how to approach it.
>
> A few of the simple background codes are:
>
> dataset <- ReadAffy() ;  myRMA <- justRMA()
>
> fit <- lmFit (myRMA, design)  # Analysis design is in object, �design�
>
> contrasts_matrix <- makeContrasts(Diseased-Healthy, levels = design)
>
>  fit2 <- contrasts.fit (fit, contrasts_matrix)
>
> fit3 <- eBayes (fit2)
>
> test_results <- topTable(fit3, number=10, adjust="BH")
>
> # Then, I was uncertain regarding how to get the output with UniGene ID.
> Wonder if a bit of tweaking in the function, probes2table should somehow
> solve this !
>
> # probes2table(****, featureNames(***), "hgu133a.db", anncols =
> aaf.handler()[c(1,2,7,9)], html = FALSE, text = TRUE, filename = "****")
>
> Many thanks,
>
> Chintanu
>
>
>
>   
>> sessionInfo ()
>>     
>
> R version 2.9.2 (2009-08-24)
>
> i386-pc-mingw32
>
> locale:
>
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
> Zealand.1252;LC_MONETARY=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
>
> attached base packages:
>
> [1] grDevices datasets  splines   graphics  stats     tcltk     utils
> methods   base
>
> other attached packages:
>
>  [1] annaffy_1.16.0       hgu133a.db_2.2.12    affycoretools_1.16.3
> KEGG.db_2.2.11       GO.db_2.2.11         RSQLite_0.7-2
> DBI_0.2-4
>
>
>  [8] AnnotationDbi_1.6.1  limma_2.18.3         hgu133acdf_2.4.0
> affy_1.22.1          Biobase_2.4.1        survival_2.35-7
>
> loaded via a namespace (and not attached):
>
>  [1] affyio_1.12.0        annotate_1.22.0      biomaRt_2.0.0
> Category_2.10.1      gcrma_2.16.0         genefilter_1.24.2
> GOstats_2.10.0
>
>  [8] graph_1.22.2         GSEABase_1.6.1       preprocessCore_1.6.0
> RBGL_1.20.0          RCurl_1.2-0          tools_2.9.2
> XML_2.6-0
>
>
> [15] xtable_1.5-5
>
> 	[[alternative HTML version deleted]]
>
>   
> ------------------------------------------------------------------------
>
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