Dear all, I am trying to use pamr.knnimpute with Agilent Microarray data which consist from 137 colums (samples) and 23653 rows (probes). These data values were calculated in log ratio, and 212 of them were "NA". I tried to run pamr.knnimpute with this dataset. But an error occurred as below. > pamr.knnimpute(tmp2) Error in rep(1, p) : invalid 'times' argument Would you tell me how to fix this problem ? Sincerely yours, Takanori Washio Keio University ------------------------------------ > tmp2[is.na(tmp2)] [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ----//---- [201] NA NA NA NA NA NA NA NA NA NA NA NA ------------------------------------ > tmp2[1,] 1 2 3 4 5 6 7 8 0.10767 0.16026 -0.04576 0.01838 0.06601 -0.01996 0.09117 0.06113 ----//---- 137 0.00153

washiot+1 at gmail.com wrote: > Dear all, > > I am trying to use pamr.knnimpute with Agilent Microarray data which > consist from 137 colums (samples) and 23653 rows (probes). > These data values were calculated in log ratio, and 212 of them were "NA". > > I tried to run pamr.knnimpute with this dataset. > But an error occurred as below. > > >>pamr.knnimpute(tmp2) > > Error in rep(1, p) : invalid 'times' argument > > > Would you tell me how to fix this problem ? You might start with the help page for pamr.knnimpute. Usage: pamr.knnimpute(data ,k = 10, rowmax = 0.5, colmax = 0.8, maxp = 1500) Arguments: data: The PAM input data. A list with components: 'x', an expression matrix with genes in the rows, samples in the columns, and 'y', a vector of the class labels for each sample. Same form as used by pamr.train, and same as that produced by 'pamr.from.excel' From what you have said, it appears that your 'tmp2' object is a matrix of expression data, not the list that pamr.knnimpute() is expecting. If you don't do what the function is expecting, it won't work correctly. Best, Jim > > > Sincerely yours, > > Takanori Washio > Keio University > > > ------------------------------------ > > >>tmp2[is.na(tmp2)] > > [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA > ----//---- > [201] NA NA NA NA NA NA NA NA NA NA NA NA > > ------------------------------------ > > >>tmp2[1,] > > 1 2 3 4 5 6 7 8 > 0.10767 0.16026 -0.04576 0.01838 0.06601 -0.01996 0.09117 0.06113 > ----//---- > 137 > 0.00153 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.