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Last seen 10.2 years ago
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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