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

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