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Question: Yeast ORF gene set analysis with globaltest (gtKEGG)
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gravatar for Rebecca Ong
16 months ago by
Rebecca Ong0 wrote:

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))

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