It is: > data <- read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', row.names = NULL ,header=TRUE, fill=TRUE) > class(data[3]) [1] "data.frame" >
And if I try to use as.matrix(read.table()), I got: >data <-as.matrix(read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', + row.names = NULL ,header=TRUE, fill=TRUE)) > 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" You see they are surrounded by "". I don't see such if I just use >read.table > data <- read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt', row.names = NULL ,header=TRUE, fill=TRUE) > 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 Thanks, Allen On Thu, Jun 12, 2008 at 7:34 PM, Erik Iverson <[EMAIL PROTECTED]> wrote: > > > ss wrote: > >> Hi Wacek, >> >> Yes, data is data frame not a matrix. >> >> is.numeric(data[3]) >>> >> [1] FALSE >> > > what is class(data[3]) > > >> But I looked at the column 3 and it looks okay though. There are few NAs >> and >> I did find >> anything strange. >> >> Any suggestions? >> >> Thanks, >> Allen >> >> >> >> On Thu, Jun 12, 2008 at 7:01 PM, Wacek Kusnierczyk < >> [EMAIL PROTECTED]> wrote: >> >> 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 >>> >>> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> 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. >> > [[alternative HTML version deleted]] ______________________________________________ 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.