[R] Problem with rowMeans()

[Wacek Kusnierczyk]

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