[BioC] Metabolomic data analysis with papi / papiHtest() does not work as expected

Carsten Jaeger [guest] guest at bioconductor.org
Thu Nov 28 19:18:24 CET 2013


Hi all,

I'm trying to analyze my metabolomic data with PAPi. All examples from the help pages of the package work fine, so my local installation seems fine. With my own dataset, everything looks fine, except for papiHtest, which only produces an empty dataframe instead of filtering out significantly different pathways. Below is a self-contained example, based on my real data. When I test results from papi() manually for significant differences, there are some. So the empty result obtained from papiHtest() is not expected.

Thanks for any help in advance!

## start example

library(PAPi)

Names <- c("Replicates", "C00385", "C00489", "C00042", "C02261", "C00149")
Sample1 <- c("cond1", "7.377297", "6.873725", "11.658225", "9.226792", "8.636739")
Sample2 <- c("cond1", "7.208188", "6.753601", "11.593091", "9.291818", "8.472792")
Sample3 <- c("cond1", "7.243537", "6.667756", "11.602593", "9.1946", "8.538539")
Sample4 <- c("cond1", "7.260916", "6.84234", "11.642048", "9.344547", "8.775064")
Sample5 <- c("cond2", "6.43645", "7.517954", "10.85541", "9.986528", "7.589869")
Sample6 <- c("cond2", "6.501811", "7.493599", "10.941813", "9.909959", "7.665613")
Sample7 <- c("cond2", "6.484239", "7.532483", "10.734369", "10.126784", "7.520619")
Sample8 <- c("cond2", "6.556364", "7.52518", "10.957901", "10.024281", "7.676388")

mydf <- data.frame(cbind(Names, Sample1, Sample2, Sample3, Sample4, 
                         Sample5, Sample6, Sample7, Sample8),
                   stringsAsFactors = FALSE)

pres <- papi(mydf, save=FALSE, offline=TRUE, localDatabase="default")

pres_sign <- papiHtest(pres, save=F)

pres_sign
## just an empty data.frame instead of significantly different pathways

## end example



 -- output of sessionInfo(): 

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
[1] PAPi_1.2.0       KEGGREST_1.2.0   svDialogs_0.9-54 svGUI_0.9-54    

loaded via a namespace (and not attached):
 [1] BiocGenerics_0.8.0 Biostrings_2.30.1  digest_0.6.3       httr_0.2          
 [5] IRanges_1.20.6     parallel_3.0.2     png_0.1-6          RCurl_1.95-4.1    
 [9] stats4_3.0.2       stringr_0.6.2      tools_3.0.2        XVector_0.2.0     

--
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