Thanks, Erik. I will try your code soon.
I did this first:
> data <-
read.table('E-TABM-1-processed-data-1342561271_log2_with_symbols.txt',
row.names = NULL ,header=TRUE, fill=TRUE)
> class(data[[3]])
[1] "factor"
> is.numeric(data[[3]])
[1] FALSE
>
So it is not numeric but 'factor' instead.
Can I convert this column to numeric?
Allen
On Thu, Jun 12, 2008 at 7:48 PM, Erik Iverson <[EMAIL PROTECTED]>
wrote:
>
>
> 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 <[EMAIL PROTECTED]<mailto:
>> [EMAIL PROTECTED]>> 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 <
>> [EMAIL PROTECTED]
>> <mailto:[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
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org <mailto:R-help@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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