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

[Aggio, Raphael]

Hi Carsten,

Thank you for the message. I believe I know the reason for this error. I am going to send you a script to try and if it works fine I can just update the version in bioconductor. I will contact you again latter today.

Cheers.
Raphael


On 28 Nov 2013, at 18:18, Carsten Jaeger [guest] <guest at bioconductor.org> wrote:

> 
> 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     
> 
> --
> Sent via the guest posting facility at bioconductor.org.