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))
