Hi all.. I'm very new R, and i'm analyzing microarray data using Bioconductor.. Recently i was given microarray data to analyze. The problem is whenever i run MAS5 presence calls algorithm, it throws an error saying NA/NaN/Inf in foreign function. How do i remove such NA/NaN/Inf's ?? I tried na.omit(dataframe) but stil problem exists. dimension of matrix (data) is 35556 7.> data.mas5calls=mas5calls(data)Getting probe level data... Computing p-values Error in FUN(1:6[[1L]], ...) : NA/NaN/Inf in foreign function call (arg 2) Thank you. -- ****************************************************************** Anand M.T School of Biotechnology (Bio-Informatics), International Instituteof Information Technology (I2IT), P-14, Rajiv Gandhi Infotech park, Hinjewadi, Pune-411 057. INDIA. "The secret of success comprised in three words.. Work, Finish & Publish" - Michael Faraday [[alternative HTML version deleted]]
On Sep 11, 2011, at 5:38 AM, anand m t wrote:> Hi all.. > I'm very new R, and i'm analyzing microarray data using Bioconductor.. > Recently i was given microarray data to analyze. The problem is > whenever i > run MAS5 presence calls algorithm, > it throws an error saying NA/NaN/Inf in foreign function. How do i > remove > such NA/NaN/Inf's ?? > I tried na.omit(dataframe) but stil problem exists. > > dimension of matrix (data) is 35556 7. > >> data.mas5calls=mas5calls(data) > Getting probe level data... > Computing p-values > Error in FUN(1:6[[1L]], ...) : > NA/NaN/Inf in foreign function call (arg 2)Besides the possibility that your data has NAs there is the possibilty that the authors of whatever package has that function did not anticipate some negative values or some other condition that your data led to. Maybe the "foreign function", i.e. not 'mas5calls' tried to take the log of 0 or some such. It's not possible to saymuch more given the vagueness of your question. This is also not the Bioconductor mailing list. -- David Winsemius, MD West Hartford, CT
Try: library(Hmisc) ?na.delete Ken Hutchison On Sep 11, 2554 BE, at 5:38 AM, anand m t <anandrox05 at gmail.com> wrote:> Hi all.. > I'm very new R, and i'm analyzing microarray data using Bioconductor.. > Recently i was given microarray data to analyze. The problem is whenever i > run MAS5 presence calls algorithm, > it throws an error saying NA/NaN/Inf in foreign function. How do i remove > such NA/NaN/Inf's ?? > I tried na.omit(dataframe) but stil problem exists. > > dimension of matrix (data) is 35556 7. > >> data.mas5calls=mas5calls(data) > Getting probe level data... > Computing p-values > Error in FUN(1:6[[1L]], ...) : > NA/NaN/Inf in foreign function call (arg 2) > > Thank you. > > -- > ****************************************************************** > Anand M.T > School of Biotechnology (Bio-Informatics), > International Instituteof Information Technology (I2IT), > P-14, Rajiv Gandhi Infotech park, > Hinjewadi, > Pune-411 057. > INDIA. > > "The secret of success comprised in three words.. Work, Finish & Publish" - > Michael Faraday > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.