[R] Problem with rowMeans()

[Erik Iverson]

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> 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 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.