Hi Wacek,
Yes, data is data frame not a matrix.
> is.numeric(data[3])
[1] FALSE
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
>
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