[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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