[BioC] Extract top-ranked genes from model fit

[James W. MacDonald]

Hi Chintanu,

Chintanu wrote:
> 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 = "****")

Did you try it? This should output probe, symbol, gene name and UniGene 
ID, without any 'tweaking' required.

Best,

Jim


> 
> 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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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826