search for: bacterial

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 c...

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 bot...

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 "...

...?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 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, i...

...rostrom 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 > >...

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 each category, with boolean entries? Or is there a way to do this more cleanly? Data file (hands.dat) ============ Bacterial.Counts Method 74 Water 84...

...dencies in Rails 0.13.1 Max bundle are now included Get it at: http://prdownloads.sourceforge.net/locomotive/Locomotive_0.2.4.dmg?download If you have any further questions, head on over to the website: http://locomotive.sourceforge.net Cheers, Ryan -- Ryan Raaum http://www.rockefeller.edu -- Bacterial Pathogenesis and Immunology http://www.worldmartial.com -- Black Belt Instructor http://locomotive.sourceforge.net -- Self contained one-click Rails for Mac OS X

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 Colv="Rowv"). The question is now, can i combine the two features that the clustering/r...

Hello everyone, I was trying to set up access control in a new application Im working on, I''m trying to use the excellent authorization plugin from Bill Katz, Its pretty straight forward to setup and should be to use. But when i try to give the same permission on two differents users on the same object i get an error. (Well , Im kinda new to all this rails stuff) r = Red.find(1) u1 =

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 <- c(2.23,0,0.03,0.71,2.34,0,0.2,0.2,0.02,2.07,0.85,0.12,0,0.59,0.02,2.3,0.29,0.39,1.32,0.07,0.52,1.2,0,0.85,1.09,0,0.5,1.4,0.08,0.11,0.0...

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 contig_type as below: AssemViral_ContigsLen<-merge(Assem_ContigsLen,allViral_contigs,by.x="contig_id",by.y="X.Contid.ID",all.x...

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 <- de...

...fety 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 pathogens. The individual works with a team of statisticians and bioinformaticians to develop and improve methods for detecting and identifying bacterial pathogens from food and environmental sources The successful applicant would be expected to effectively interact wit...

Hello everybody, I'm testing the randomForest package in order to do some simulations and I get some trouble with the prediction of new values. The random forest computation is fine but each time I try to predict values with the newly created object, I get an error message. I thought I was because NA values in the dataframe, but I cleaned them and still got the same error. What am I

Hi: I love Locomotive and use it exclusively for my rails projects. I''d like to install GRUFF and give it a try (a graph image creation package). I know I can do sudo gem install gruff from the command line for normal ruby and rails. How do I make gems available to Locomotive? bruce

...neither. Gotchas ======= * Older server bundles may not work properly. (Older rails bundles should be fine). With Code Contributions from: ====================== * Tobias Lidskog * DeLynn Berry * Thomas Steinhausen * Sammi Williams Cheers! -ryan -- Ryan Raaum http://www.rockefeller.edu -- Bacterial Pathogenesis and Immunology http://www.worldmartial.com -- Black Belt Instructor http://locomotive.sourceforge.net -- Self contained one-click Rails for Mac OS X

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 samples will generate the following concentrations: 1, 1/2, 1.4, 1/8, 1/16, ... (or the reciprocal: 1, 2, 4, 8, 16, ...) It makes no sense to compute the arithmetic mean. Results a...

...3.026e+09 3rd Qu.:7.699e+09 11 : 1 Ma,6 :10 6 :12 Max. :8.7375 Max. :3.296e+09 Max. :8.501e+09 (Other):114 (Other):60 (Other):48 uid = unique id for an observation cid = culture id (a within subjects factor identifying each bacterial culture) date = date of culture; data was collected in 2 batches, with a balanced split of observations (3 replicates of each genotype in each batch) g = genotype (the name of the bactrial strain) t = time (1-10 hours) od = optical density (a proxy for poulation density of the bacte...

...component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate a heatmap from a table that contains the abundance of different bacteria at different locations, with a dendrogram that groups the environments by the pattern of bacterial abundance. This is easy, thanks to a nice code snippet at the R Graph Gallery (http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=66): env <- read.table("env.dat") x <- as.matrix(env) hv <- heatmap(x, col = cm.colors(256), scale="none", xlab...

...o work with. I specify it here to illustrate that it is not always obvious what the bounds on the parameters are. SSbaranyiBR94<-selfStart( model=function(Time, y0, ymax, mu, lambda, m = 1, v = mu) { #+ # From the paper Baranyi J. & Roberts T. A. (1994). A dynamic approach to predicting bacterial growth in food. Int J. of Fd. Micro. 23. 277-294 # Papers equations (6), (5b), (4b) # eq 4b: y(Time) = y0 + mu' * A(Time) - ln(1+(exp(m' * mu' * A(Time)) - 1)/exp(m' * (ymax-y0)))/m' # eq 5b: A(Time) = Time + ln((exp(-v * Time) + q0)/(1+ q0))/v # from eq 6: q0 = 1/(exp(mu...