Hi Raphael, thanks for your prompt answer. The script works fine, both for the example and my full dataset. Results look plausible. Best Carsten On Fri, Nov 29, 2013 at 2:04 PM, Raphael Aggio <raphael.aggio@gmail.com>wrote: > 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@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 > [[alternative HTML version deleted]]