ss wrote:
> Thank you very much, Wacek! It works very well.
> But there is a minor problem. I did the following:
>
> >data <-
> read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt',
> +row.names = NULL ,header=TRUE, fill=TRUE)looks like you have a data frame, not a matrix > > dim(data) > [1] 23963 85 > > data[1:4,1:4] > Probe_ID Gene_Symbol M16012391010920 M16012391010525 > 1 A_23_P105862 13CDNA73 -1.6 0.16 > 2 A_23_P76435 15E1.2 0.18 0.59 > 3 A_24_P402115 15E1.2 1.63 -0.62 > 4 A_32_P227764 15E1.2 -0.76 -0.42 > >data1<-data[sapply(data, is.numeric)] > > dim(data1) > [1] 23963 82 > > data1[1:4,1:4] > M16012391010525 M16012391010843 M16012391010531 M16012391010921 > 1 0.16 -0.23 -1.40 0.90 > 2 0.59 0.28 -0.30 0.08 > 3 -0.62 -0.62 -0.22 -0.18 > 4 -0.42 0.01 0.28 -0.79 > > You will notice that, after using 'data[sapply(data, is.numeric)]' and > getting > data1, the first sample in data, called 'M16012391010920', was missed > in data1. > > Any further suggestions? > surely there must be an entry in column 3 that makes it non-numeric. what does is.numeric(data[3]) say? (NAs should not make a column non-numeric, unless there are only NAs there, which is not the case here.) check your data for non-numeric entries in column 3, there can be a typo. vQ ______________________________________________ R-help@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.
