[R] Question about correlation

[Jim Lemon]

I think that Goran is right, I didn't take "cor(data)" literally.

Jim


On Thu, Jul 6, 2017 at 3:38 AM, Göran Broström <goran.brostrom at umu.se> wrote:
> On 2017-07-05 11:56, Jim Lemon wrote:
>>
>> Hi Chin Yi,
>> If you are trying to correlate "Health" with "Disease", i.e.
>>
>> cydf<-read.table(text="OTU ID Health Disease
>>    Bacterial 1 0.29 0.34
>>    Bacterial 2 0.25 0.07
>>    Bacterial 3 0.06 0.06
>>    Bacterial 4 0.07 0.09
>>    Bacterial 5 0.02 0.05",
>>    header=TRUE)
>> print(cor(cydf$Health,cydf$Disease))
>> [1] 0.7103517
>>
>> If you are getting that error, it probably means that either "Health"
>> or "Disease" or perhaps both have been read in as a factor. To test
>> this:
>>
>> is.factor(cydf$Health)
>> [1] FALSE
>>>
>>> is.factor(cydf$Disease)
>>
>> [1] FALSE
>>
>> If either of these returns TRUE, that is almost certainly the problem.
>
>
> Or maybe Chin Yi tried (as it seems)
>
>> cor(cydf)
> Error in cor(cydf) : 'x' must be numeric
>
> (with cydf == data): 'OTU' is not numeric.
>
> Follow Jim's advice.
>
> Göran
>
>
>>
>> Jim
>>
>>
>> On Wed, Jul 5, 2017 at 11:27 AM, SEB140004 Student
>> <chinyi at siswa.um.edu.my> wrote:
>>>
>>> Greeting.
>>>
>>> Dear Mr/Mrs/Miss,
>>>
>>> OTU ID Health Disease
>>> Bacterial 1 0.29 0.34
>>> Bacterial 2 0.25 0.07
>>> Bacterial 3 0.06 0.06
>>> Bacterial 4 0.07 0.09
>>> Bacterial 5 0.02 0.05
>>> Above show the first 6 data sets, may I ask that the reason of R show the
>>> error like "Error in cor(data) : 'x' must be numeric" ? And how to solve
>>> it? Besides, isn't this data can conduct correlation matrix?
>>>
>>> Moreover, isn't this data sets can be plot into network? If can, which
>>> package should I use?
>>>
>>> Thank you.
>>>
>>> Best regards,
>>> Kang Chin Yi
>>>
>>>          [[alternative HTML version deleted]]
>>>
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>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.