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

Raphael Aggio raphael.aggio at gmail.com
Fri Nov 29 14:04:26 CET 2013


Hey Carsten,

Thank you for the message. Could you please try the script attached? If it
works fine for you I can update it in Bioconductor.

To try it, you can use:

source("path to the file attached")

testingHtest(pres, save = F)

Cheers.
Raphael


On 28 November 2013 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.
>



-- 
Raphael Aggio
Research Associate
Department of Gastroenterology
University of Liverpool
Nuffield Building
Crown Street
Liverpool L693GE


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