Question: [maSigPro] Error in T.fit - NAs introduced by coercion
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gravatar for Maciej Jończyk
9.5 years ago by
Maciej Jończyk720 wrote:
Dear list Members, I use maSigPro package, in T.fit I've got following warning message: There were 50 or more warnings (use warnings() to see the first 50) > warnings() Warning messages: 1: In rbind(sol, as.numeric(c(p.value, result$r.squared, ... : NAs introduced by coercion 2: In rbind(sol, as.numeric(c(p.value, result$r.squared, ... : NAs introduced by coercion ... I've searched the archive and I found that warning message containing "NAs introduced by coercion" happens also in other functions. Is it problem with coercion of data to matrix, i.e. command takes character column as a numeric one? My data desn't have NAs. Input to this command (T.fit) is an output of previous steps in ordinary maSigPro workflow (without errors/warnings), so I think data itself is correct. I'm not very experienced in programming and maybe there is an easy solution. I would like to ask for advice. Is it a serious warning (in object created in T.fit indeed are NAs)? Can I do something to avoid it? Here is my session info (two, because I run analysis on two computers and problem appears on both). > sessionInfo() R version 2.11.0 (2010-04-22) i486-pc-linux-gnu locale: [1] LC_CTYPE=pl_PL.UTF-8 LC_NUMERIC=C [3] LC_TIME=pl_PL.UTF-8 LC_COLLATE=pl_PL.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=pl_PL.UTF-8 [7] LC_PAPER=pl_PL.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] maSigPro_1.20.0 DynDoc_1.26.0 widgetTools_1.26.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] limma_3.4.0 Mfuzz_2.6.0 tkWidgets_1.26.0 > sessionInfo() R version 2.10.0 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] maSigPro_1.18.0 DynDoc_1.24.0 widgetTools_1.24.0 Biobase_2.6.1 loaded via a namespace (and not attached): [1] limma_3.2.3 Mfuzz_2.4.0 tkWidgets_1.24.0 Best Regards, Maciej Jo?czyk, MSc Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 ___________________________________ NOCC, http://nocc.sourceforge.net -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com
masigpro • 996 views
ADD COMMENTlink modified 9.5 years ago by Mª José Nueda90 • written 9.5 years ago by Maciej Jończyk720
Answer: [maSigPro] Error in T.fit - NAs introduced by coercion
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gravatar for Mª José Nueda
9.5 years ago by
Spain
Mª José Nueda90 wrote:
Dear Maciej, This warning is not a problem. The output of T.fit function is a list. One object of this list, named "sol", contains the p-vaules of the variables that the stepwise strategy decides to include in the model. So the variables that are not considered don't have any p-value to show and we decided to put "NA". Doing this R always show this warning, but for maSigPro this is not an error, it is normal. Regards, Mar?a Jos? Nueda. ----- Original Message ----- From: "Maciej Jo?czyk" <mjonczyk@biol.uw.edu.pl> To: <bioconductor at="" stat.math.ethz.ch=""> Cc: "Maciej Jo?czyk" <mjonczyk at="" biol.uw.edu.pl=""> Sent: Wednesday, April 28, 2010 10:47 PM Subject: [BioC] [maSigPro] Error in T.fit - NAs introduced by coercion > Dear list Members, > > I use maSigPro package, in T.fit I've got following warning message: > > There were 50 or more warnings (use warnings() to see the first 50) >> warnings() > Warning messages: > 1: In rbind(sol, as.numeric(c(p.value, result$r.squared, ... : > NAs introduced by coercion > 2: In rbind(sol, as.numeric(c(p.value, result$r.squared, ... : > NAs introduced by coercion > ... > > I've searched the archive and I found that warning message containing > "NAs introduced by coercion" happens also in other functions. > > Is it problem with coercion of data to matrix, i.e. command takes > character column as a numeric one? My data desn't have NAs. > > Input to this command (T.fit) is an output of previous steps in ordinary > maSigPro workflow (without errors/warnings), so I think data itself is > correct. > > I'm not very experienced in programming and maybe there is an easy > solution. > I would like to ask for advice. > Is it a serious warning (in object created in T.fit indeed are NAs)? Can > I do something to avoid it? > > Here is my session info (two, because I run analysis on two computers > and problem appears on both). > >> sessionInfo() > R version 2.11.0 (2010-04-22) > i486-pc-linux-gnu > > locale: > [1] LC_CTYPE=pl_PL.UTF-8 LC_NUMERIC=C > [3] LC_TIME=pl_PL.UTF-8 LC_COLLATE=pl_PL.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=pl_PL.UTF-8 > [7] LC_PAPER=pl_PL.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] maSigPro_1.20.0 DynDoc_1.26.0 widgetTools_1.26.0 > Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] limma_3.4.0 Mfuzz_2.6.0 tkWidgets_1.26.0 > > > >> sessionInfo() > R version 2.10.0 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] maSigPro_1.18.0 DynDoc_1.24.0 widgetTools_1.24.0 > Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] limma_3.2.3 Mfuzz_2.4.0 tkWidgets_1.24.0 > > > > Best Regards, > > Maciej Jo?czyk, MSc > Department of Plant Molecular Ecophysiology > Institute of Plant Experimental Biology > Faculty of Biology, University of Warsaw > 02-096 Warszawa, Miecznikowa 1 > > > > ___________________________________ > NOCC, http://nocc.sourceforge.net > > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.5 years ago by Mª José Nueda90
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