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Did you try -log(p)? This should work provided the zeros you report below aren't really zero. Best, Jim Li, Aiguo (NIH/NCI) [C] wrote: > Dear all, > > > > I have a list of p values as below and would like to convert it into > minus log p. How should I do it in R? > > > > Thanks in advance, > > > > AG Lee > > > > 0 > > 0.069805 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0.176752 > > 0.049759 > > 0.143271 > > 0.122581 > > 0.012448 > > 0.037795 > > 0 > > 0.004878 > > 0.319481 > > 0.07681 > > 0.106322 > > 0.005626 > > 0.852804 > > 0.011966 > > 0.197347 > > 0.081081 > > 0.809278 > > 0.012658 > > 0.190164 > > 0.010417 > > 0.242424 > > 0.003454 > > 0.211268 > > 0.257426 > > 0.287611 > > 0.455696 > > 0 > > 0.822715 > > 0.692568 > > 0.141827 > > 0.053435 > > 0.211744 > > 0.002809 > > 0 > > 0.897356 > > 0.052373 > > 0.077544 > > 0.015652 > > 0 > > 0.115321 > > 0.415888 > > 0 > > 0.854914 > > 0 > > 0.173913 > > 0.926509 > > 0.007704 > > 0.144578 > > 0.071186 > > 0 > > 0.343849 > > 0.545757 > > 0 > > 0.09913 > > 0.056106 > > 0.088586 > > 0.942356 > > 0.249117 > > 0 > > 0.438356 > > 0.673736 > > 0.017857 > > 0.22973 > > 0.203306 > > 0.027553 > > 0.872822 > > 0.387987 > > 0.11324 > > 0.033762 > > 0.106796 > > 0.219585 > > 0 > > 0.365052 > > 0.03405 > > 0.261111 > > 0.913559 > > 0.017945 > > 0.004951 > > 0 > > 0.015038 > > 0.066884 > > 0.138748 > > 0.213287 > > 0.01071 > > 0.028668 > > 0.115587 > > 0.830846 > > 0.015152 > > 0.71 > > 0 > > 0.060606 > > 0.190554 > > 0.156627 > > 0.00821 > > 0.031949 > > 0.866005 > > 0.00361 > > 0.008562 > > 0.340836 > > 0.02916 > > 0.46677 > > 0.328205 > > 0.049404 > > 0.588618 > > 0.008902 > > 0.614238 > > 0.612795 > > 0.155673 > > 0.003077 > > 0.633157 > > 0.685864 > > 0.54321 > > 0.015437 > > 0.014085 > > 0.983452 > > 0 > > 0.72758 > > 0.407718 > > 0.153199 > > 0.528875 > > 0.563679 > > 0 > > 0.056899 > > 0.073552 > > 0.476271 > > 0.126904 > > 0.003115 > > 0.268608 > > 0.571207 > > 0.02139 > > 0.135987 > > 0.037705 > > 0.005076 > > 0.017268 > > 0.269663 > > 0.00846 > > 0.095638 > > 0.00624 > > 0.817708 > > 0.801038 > > 0.343333 > > 0.641538 > > 0 > > 0.011349 > > 0.005181 > > 0.098361 > > 0.048991 > > 0.017301 > > 0.306733 > > 0.222222 > > 0.327243 > > 0.001504 > > 0.004666 > > 0.015912 > > 0 > > 0.312 > > 0.046823 > > 0.076299 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

Hi, Paste the following code, and the -log values is in the object "logged"... paste all the below code: AGLee <- scan(nlines=167,what=list(0)) 0 0.069805 0 0 0 0 0 0 0 0.176752 0.049759 0.143271 0.122581 0.012448 0.037795 0 0.004878 0.319481 0.07681 0.106322 0.005626 0.852804 0.011966 0.197347 0.081081 0.809278 0.012658 0.190164 0.010417 0.242424 0.003454 0.211268 0.257426 0.287611 0.455696 0 0.822715 0.692568 0.141827 0.053435 0.211744 0.002809 0 0.897356 0.052373 0.077544 0.015652 0 0.115321 0.415888 0 0.854914 0 0.173913 0.926509 0.007704 0.144578 0.071186 0 0.343849 0.545757 0 0.09913 0.056106 0.088586 0.942356 0.249117 0 0.438356 0.673736 0.017857 0.22973 0.203306 0.027553 0.872822 0.387987 0.11324 0.033762 0.106796 0.219585 0 0.365052 0.03405 0.261111 0.913559 0.017945 0.004951 0 0.015038 0.066884 0.138748 0.213287 0.01071 0.028668 0.115587 0.830846 0.015152 0.71 0 0.060606 0.190554 0.156627 0.00821 0.031949 0.866005 0.00361 0.008562 0.340836 0.02916 0.46677 0.328205 0.049404 0.588618 0.008902 0.614238 0.612795 0.155673 0.003077 0.633157 0.685864 0.54321 0.015437 0.014085 0.983452 0 0.72758 0.407718 0.153199 0.528875 0.563679 0 0.056899 0.073552 0.476271 0.126904 0.003115 0.268608 0.571207 0.02139 0.135987 0.037705 0.005076 0.017268 0.269663 0.00846 0.095638 0.00624 0.817708 0.801038 0.343333 0.641538 0 0.011349 0.005181 0.098361 0.048991 0.017301 0.306733 0.222222 0.327243 0.001504 0.004666 0.015912 0 0.312 0.046823 0.076299 aglee=as.data.frame(AGLee) logged=-log(aglee) print("Bioconductor is King") > Dear all, > > > > I have a list of p values as below and would like to convert it into > minus log p. How should I do it in R? > > > > Thanks in advance, > > > > AG Lee > > > > 0 > > 0.069805 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0 > > 0.176752 > > 0.049759 > > 0.143271 > > 0.122581 > > 0.012448 > > 0.037795 > > 0 > > 0.004878 > > 0.319481 > > 0.07681 > > 0.106322 > > 0.005626 > > 0.852804 > > 0.011966 > > 0.197347 > > 0.081081 > > 0.809278 > > 0.012658 > > 0.190164 > > 0.010417 > > 0.242424 > > 0.003454 > > 0.211268 > > 0.257426 > > 0.287611 > > 0.455696 > > 0 > > 0.822715 > > 0.692568 > > 0.141827 > > 0.053435 > > 0.211744 > > 0.002809 > > 0 > > 0.897356 > > 0.052373 > > 0.077544 > > 0.015652 > > 0 > > 0.115321 > > 0.415888 > > 0 > > 0.854914 > > 0 > > 0.173913 > > 0.926509 > > 0.007704 > > 0.144578 > > 0.071186 > > 0 > > 0.343849 > > 0.545757 > > 0 > > 0.09913 > > 0.056106 > > 0.088586 > > 0.942356 > > 0.249117 > > 0 > > 0.438356 > > 0.673736 > > 0.017857 > > 0.22973 > > 0.203306 > > 0.027553 > > 0.872822 > > 0.387987 > > 0.11324 > > 0.033762 > > 0.106796 > > 0.219585 > > 0 > > 0.365052 > > 0.03405 > > 0.261111 > > 0.913559 > > 0.017945 > > 0.004951 > > 0 > > 0.015038 > > 0.066884 > > 0.138748 > > 0.213287 > > 0.01071 > > 0.028668 > > 0.115587 > > 0.830846 > > 0.015152 > > 0.71 > > 0 > > 0.060606 > > 0.190554 > > 0.156627 > > 0.00821 > > 0.031949 > > 0.866005 > > 0.00361 > > 0.008562 > > 0.340836 > > 0.02916 > > 0.46677 > > 0.328205 > > 0.049404 > > 0.588618 > > 0.008902 > > 0.614238 > > 0.612795 > > 0.155673 > > 0.003077 > > 0.633157 > > 0.685864 > > 0.54321 > > 0.015437 > > 0.014085 > > 0.983452 > > 0 > > 0.72758 > > 0.407718 > > 0.153199 > > 0.528875 > > 0.563679 > > 0 > > 0.056899 > > 0.073552 > > 0.476271 > > 0.126904 > > 0.003115 > > 0.268608 > > 0.571207 > > 0.02139 > > 0.135987 > > 0.037705 > > 0.005076 > > 0.017268 > > 0.269663 > > 0.00846 > > 0.095638 > > 0.00624 > > 0.817708 > > 0.801038 > > 0.343333 > > 0.641538 > > 0 > > 0.011349 > > 0.005181 > > 0.098361 > > 0.048991 > > 0.017301 > > 0.306733 > > 0.222222 > > 0.327243 > > 0.001504 > > 0.004666 > > 0.015912 > > 0 > > 0.312 > > 0.046823 > > 0.076299 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > > . > >