Hi James

Thanks a lot for that. I also found out that I could use
stringsAsFactors=FALSE in the read.table command. I appologize for
reposting an already answered question.

Thanks a lot
yours,
Alyaa


On Tue, Nov 13, 2012 at 9:45 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Alyaa,
>
> See here:
>
> http://cran.r-project.org/doc/**FAQ/R-FAQ.html#How-do-I-**
> convert-factors-to-numeric_**003f<http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-convert-factors-to-numeric_003f>
>
> Best,
>
> Jim
>
>
>
>
> On 11/13/2012 1:52 PM, Alyaa Mahmoud wrote:
>
>> Dear All
>>
>> I have a dataframe (data) with numeric values. However, when I run pvclust
>> i get the error:
>>
>>  pv<- pvclust(as.matrix(data), method.dist="correlation",
>>>
>> method.hclust="complete", nboot=10)
>> Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric
>>
>> I tried to convert to numeric using as.numeric:
>> data[,1:5] = lapply(data[,1:5], as.numeric) but the values change if I do
>> this ?????
>>
>> Anybody knows why would the values change when I use as.numeric ?? How can
>> I convert the values to "numeric" without changing them then ??
>>
>>  data
>>>
>>            TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01
>> 1053_at               *6.78057386468964*             7.20429615680331
>>
>> 117_at                 4.5369738739652             5.71461488261629
>> 121_at                 5.7547177840092             6.27768302308676
>> 1255_g_at             3.51242959009833             4.38185514015951
>> 1294_at               5.71812084213166             5.18297525921706
>>            TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01
>> 1053_at               6.32600010999327             7.36481160075073
>> 117_at                 4.8915996267868             4.91877155427287
>> 121_at                6.22521524027822             5.92939849291023
>> 1255_g_at             5.81450662569868             3.56178691911277
>> 1294_at               5.94603190363047             5.08045063963826
>>            TCGA.06.0178.01A.01R.0233.01
>> 1053_at               7.08406595975373
>> 117_at                4.45519578310485
>> 121_at                6.98951423954871
>> 1255_g_at             3.41240570036661
>> 1294_at               6.19723107114317
>>
>>> pv<- pvclust(as.matrix(data), method.dist="correlation",
>>>
>> method.hclust="complete", nboot=10)
>> Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric
>>
>>> *data[,1:5] = lapply(data[,1:5], as.numeric)*
>>> data
>>>
>>            TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01
>> 1053_at                          *15129 *                       16227
>>
>> 117_at                            9527                        12658
>> 121_at                           12662                        13992
>> 1255_g_at                         2970                         8963
>> 1294_at                          12578                        11398
>>            TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01
>> 1053_at                          14118                        16721
>> 117_at                           10585                        10885
>> 121_at                           13874                        13334
>> 1255_g_at                        12852                         2937
>> 1294_at                          13197                        11307
>>            TCGA.06.0178.01A.01R.0233.01
>> 1053_at                          16314
>> 117_at                            8829
>> 121_at                           16074
>> 1255_g_at                         1765
>> 1294_at
>>
>>
>> Thanks a lot
>> yours,
>> Alyaa
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>


-- 
Alyaa Mahmoud

"Love all, trust a few, do wrong to none"- Shakespeare

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