Yeast ORF gene set analysis with globaltest (gtKEGG)
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@rebecca-ong-11099
Last seen 5.2 years ago

I'm attempting to use globaltest and the gtKEGG function for gene set analysis using the KEGG pathways. My data is comparing differential expression of different Saccharomyces cerevisiae genes (columns - labeled with ORF#) for samples in two categories (0 and 1). Here is a brief snapshot of my data:

<caption>Raw Data</caption>
Levels YNL106C YOR311C YHL009C YBR263W
0 0.3 -2.5 3.4 -0.6
0 0.3 -1.1 2.1 -0.9
0 0.7 -2.4 2.6 -3.4
1 -0.8 -1.1 -2.0 -0.3
1 -0.8 1.0 -3.0 -0.2
1 -0.6 1.7 -3.0 1.2

The expression data is stored in a data frame of numbers (CG) and the levels are stored as a vector of factors (CGFactors).

I am able to run: gt(CGFactors, CG).

When I run gtKEGG I get the following error: 

>gtKEGG(CGFactors,CG, annotation = "org.Sc.sgd.db")

Error in eval(expr, envir, enclos) : object 'org.Sc.sgdPATH2EG' not found

This is because the yeast annotation database uses ORF and so the mappings are labeled differently. The comparable pathway for yeast is: "org.Sc.sgdPATH2ORF"

However I have not been able to figure out how to incorporate this into the gtKEGG function. The following does not work: 

>gtKEGG(CGFactors,CG, annotation = as.list(org.Sc.sgdPATH2ORF))

This basically spits out a huge set of errors.

Does anyone have any idea how to adapt gtKEGG to work with the yeast database (org.Sc.sgd.db)?

Thanks,


Rebecca Ong
Research Assistant Professor
Michigan State University

 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices
[6] utils     datasets  methods   base     

other attached packages:
[1] org.Sc.sgd.db_3.3.0  AnnotationDbi_1.34.4
[3] IRanges_2.6.1        S4Vectors_0.10.2    
[5] Biobase_2.32.0       BiocGenerics_0.18.0 
[7] globaltest_5.26.0    survival_2.39-5     

loaded via a namespace (and not attached):
 [1] lattice_0.20-33 XML_3.98-1.4    grid_3.3.1     
 [4] xtable_1.8-2    DBI_0.4-1       RSQLite_1.0.0  
 [7] annotate_1.50.0 Matrix_1.2-6    splines_3.3.1  
[10] tools_3.3.1    

For the first error:
> traceback()
3: eval(expr, envir, enclos)
2: evalas.name(paste(annotation, extension, sep = "")))
1: gtKEGG(CGFactors, CG, annotation = "org.Sc.sgd.db")

For the second error:
> traceback()
2: stop("package ", package, " is not available")
1: gtKEGG(CGFactors, CG, annotation = as.list(org.Sc.sgdPATH2ORF))

globaltest saccharomyces cerevisiae gtKEGG KEGG gene set analysis • 652 views
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