Question: Metabolomic data analysis with papi / papiHtest() does not work as expected
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5.7 years ago by
Guest User12k
Guest User12k 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.
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ADD COMMENTlink modified 5.7 years ago by Aggio, Raphael20 • written 5.7 years ago by Guest User12k
Answer: Metabolomic data analysis with papi / papiHtest() does not work as expected
1
gravatar for Aggio, Raphael
5.7 years ago by
Aggio, Raphael20 wrote:
Hi Carsten, Thank you for the message. I believe I know the reason for this error. I am going to send you a script to try and if it works fine I can just update the version in bioconductor. I will contact you again latter today. Cheers. Raphael On 28 Nov 2013, at 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.
ADD COMMENTlink written 5.7 years ago by Aggio, Raphael20
Answer: Metabolomic data analysis with papi / papiHtest() does not work as expected
0
gravatar for Raphael Aggio
5.7 years ago by
Raphael Aggio30 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 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
ADD COMMENTlink written 5.7 years ago by Raphael Aggio30
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]]
ADD REPLYlink written 5.7 years ago by Carsten Jaeger10
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