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]]
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. 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]] > > ______________________________________________ > 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.
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. G?ran> > 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]] >> >> ______________________________________________ >> 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. >
Please keep the conversation on the list: Others may be able to help you better than I can. On 2017-07-06 10:38, SEB140004 Student wrote:> Ya. I had successfully got the result. Thank you very much. :) > > Isn't possible for me to obtain the network from the correlation matrix?I know nothing about correlation networks, but by googling I found two R packages, ggraph and corrr, that may be of interest to you. G?ran> On Thu, Jul 6, 2017 at 1:38 AM, G?ran Brostr?m <goran.brostrom at umu.se > <mailto: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. > > G?ran > > > > Jim > > > On Wed, Jul 5, 2017 at 11:27 AM, SEB140004 Student > <chinyi at siswa.um.edu.my <mailto: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]] > > ______________________________________________ > R-help at r-project.org <mailto:R-help at r-project.org> mailing > list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > <https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > <http://www.R-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible > code. > > > ______________________________________________ > R-help at r-project.org <mailto:R-help at r-project.org> mailing list > -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > <https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > <http://www.R-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. > >