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]]

