similar to: Question about correlation

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

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) >

Greeting. Dear Mr/Mrs/Miss, I want to create a network by using R but I only have a table that contain OTU ID and the abundance value of two samples ONLY. Isn't possible? If can, which package can be used? Greatly appreciated to any suggestions and helps. Thank you. Best regards, Kang Chin Yi [[alternative HTML version deleted]]

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,

I think that Goran is right, I didn't take "cor(data)" literally. Jim On Thu, Jul 6, 2017 at 3:38 AM, G?ran Brostr?m <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

I have data in a file named hands.dat, which is given at the end of this question. (It's from a stats textbook example on anova). I'd like to do an aov on this, which I guess would be d <- read.table("~/hands.dat", header=TRUE) aov(Bacterial.Counts ~ Water + Soap + Antibacterial.Soap + Alcohol.Spray, data=d) but this fails. Do I need to break d$Method up into columns for

I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you library(vegan) gotud <-

Dear all, I am interested in correctly testing effects of continuous environmental variables and ordered factors on bacterial abundance. Bacterial abundance is derived from counts and expressed as percentage. My problem is that the abundance data contain many zero values: Bacteria <-

I am pleased to announce the newest release of Locomotive! http://locomotive.sourceforge.net Mostly a bug fix release. If you are using Locomotive on 10.4 you should definitely upgrade. New in 0.2.4 ============ * Rename application entries in status window * Run/Restart/Stop buttons now immediately update * Bundle choosing is fixed for Mac OS X 10.4 * Missing gem dependencies in Rails 0.13.1

Hi all, I have 6 datasets(dataframes Assem_ContigsLen7 through all_ContigsLen12) containing 3 columns (contig_id, contig_length, read_count). Each dataset is composed of 3 types of contigs (assemblies of genomic fragments), 1- all Bacterial fragments, 2 - all Viral fragments, 3 - mixed fragments. I identified the type of contig through a merge with another table with just contig_id and

I am trying to input an OTU table into EstimateS, however, the format of the OTU table has to be changed to fit the format EstimateS will accept. In R, I would like to change the format of the OTU table (from excel). Here is what I need to do, take Example 1 and create Example 2. The problem is that I have hundreds of OTUs, so I can't do this by hand (and I'd love to have a code that I

Hi All, I''m very happy to announce the release of Locomotive 1.0.0. Locomotive is a one-click development solution for Rails on Mac OS X. See more details at http://locomotive.sourceforge.net Get it at: http://prdownloads.sourceforge.net/locomotive/Locomotive_1.0.0.dmg?download What''s New? =========== * Server bundle updated to lighttpd 1.4.8 * Server bundle updated to

Hello! I am eager to learn if I only have a data about the relationship between otu and sample, could I use the function capscale, and final make a point plot that x-axis is CAP1 and y-axis is CAP2? Besides, what function could I use to make the different rarefaction curve with different color in the a plot in R? Appreciate very much.

Dear Rich, It depends how the data is generated. Although I am not an expert in ecology, I can explain it based on a biomedical example. Certain variables are generated geometrically (exponentially), e.g. MIC or Titer. MIC = Minimum Inhibitory Concentration for bacterial resistance Titer = dilution which still has an effect, e.g. serially diluting blood samples; Obviously, diluting the

Hi there, I have two questions about heatmap.2 in gplot. My input is a simple square matrix with numeric values between 75 and 100 (it is a similarity matrix based on bacterial DNA sequences). 1. I can sort my input matrix into categories with rowsidecolors (in this case, very conveniently by bacterial taxa). I do a clustering and reordering of my matrix by Rowv=TRUE (and

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hi Everyone, I posted this a couple of weeks ago with no responses. My interface (via gmane) seemed a bit flakey at the time, so I'm venturing to repost with some additional information. I'm trying to write selfStart non-linear models for use with nls. In these models some combinations of parameter values are illegal; the function value is undefined. That's OK when calling the

Hi all, I have the following setup PSTN -> ASTERISK -> IVR (using dialogic card) 1) Caller id information is presented to asterisk during the first and second ring. 2) Hence, Asterisk waits for 2 rings before pickup the call and forwarding to the appropriate FXS port. 3) The IVR application also waits for 2 rings before picking up the call to get the caller id. 4) Hence any caller

Hi, everyone: R is new to me. I am writing a nested loop to simulate data for t-test. The following code is wrong. The subscript is out of bounds. Could anyone tell me how to revise it? Thanks, Riddle Chin. result<-matrix(ncol=5, nrow=1000) colnames(result)<-c('N=20','N=40','N=60','N=80','N=100') for (i in 1:1000){ for (j in

The Biostatistics Analytics Team at the FDA Center for Food Safety and Applied Nutrition seeks an MS/PhD in computer science (or related field) with experience in bioinformatics. The Analytics Team is responsible for computational support for projects involving large chemical and microbial hazard data sets, including bioinformatic and statistical analysis of bacterial genomic data for foodborne