Re: [R] Problem with rowMeans()

From: ss <affysnp_at_gmail.com>
Date: Thu, 12 Jun 2008 19:38:20 -0400

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 <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> 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]]
>>
>> ______________________________________________
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>> PLEASE do read the posting guide
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>>
>

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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 Thu 12 Jun 2008 - 23:40:37 GMT

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