From: Erik Iverson <iverson_at_biostat.wisc.edu>

Date: Thu, 12 Jun 2008 18:48:25 -0500

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. Received on Fri 13 Jun 2008 - 01:13:43 GMT

Date: Thu, 12 Jun 2008 18:48:25 -0500

ss wrote:

*> 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"
**> >
**>
*

Oops, should have said class(data[[3]]) and is.numeric(data[[3]])

See ?Extract

*>
*

> 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
**>
*

That is because matrices (objects of class 'matrix') are of homogeneous type. It changes everything to a character (including the numbers), which you certainly do NOT want.

You want a data.frame, I will provide an example of what I think you are after.

Try the following commands and see how they compare to your situation: these work for me.

test <- data.frame(x = factor(rep(c("A", "B"), each = 13)), y = rnorm(26), z = rnorm(26))

test

class(test)

is.numeric(test[[2]])

is.numeric(test[[3]])

rowMeans(test)

rowMeans(test[2:3])

*> > 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 <iverson_at_biostat.wisc.edu
**> <mailto:iverson_at_biostat.wisc.edu>> 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 <
**> Waclaw.Marcin.Kusnierczyk_at_idi.ntnu.no
**> <mailto:Waclaw.Marcin.Kusnierczyk_at_idi.ntnu.no>> 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_at_r-project.org <mailto: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.
**>
*

>

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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. Received on Fri 13 Jun 2008 - 01:13:43 GMT

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