search for: otu

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,...

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? Be...

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,...

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 &quo...

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....

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]]

...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 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 >> &...

...trom 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))...

Hello, I calculate the correlation between two matrices cor(x,y, method="spearman") and I am wondering if it possible to see only the significant correlations. I can do that for single OTUs with cor.test() command but I would like to have an output for whole matrix. Besides,I would like to plot the relative abundance of each OTU, against the number of significant pair-wise correlations to other OTUs. However, I do not know how to introduce p <.05 parameter in the script. Thank yo...

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16 different species (OTUs). Firstly I want to make a nmds plot and see how different the treatments are. Meaning how the species covaries with the environment...

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 <- decostand(gotu,"hell") G.var <- varpart(gotud,~Depth,~CH4_oxidati...

I have two data matrices that I want to make the correlation between each column from data1 and each column from data 2 and also calculate the p-value Matrices dont have the same size and I tried such a script. > bg <- read.table (file.choose(), header=T, row.names) > bg > Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 > Gi20Jun11 0.001217 0 0.001217 0 0.000000 0 0 0 0.001217 0 0 0 0 0 0.001217 0 0.001217 > Gi40Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000...

Hello, I am a relatively new R-user who has a lot to learn. I have a large dataset that is in the following dataframe format: red A B C green D blue E F Where red, green and blue are "species" names and A, B and C are observations (corresponding to DNA sequences). Each observation can only belong to one species. I would like to list the observations in one column, with the species

Dear list, When compiling the R-2.3.0 on FC4 x86_64, I got the following errors: make[3]: Entering directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' gcc -Wl,--export-dynamic -L/usr/local/lib64 -o R.bin Rmain.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o

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Hello list. I'm trying to rebuild the 2.6.9.67.0.20.EL kernel, but it fails even without modifications. How did I try it? Created a (non-root) build environment (not a mock ) Installed the kernel.scr.rpm and did a rpmbuild -ba --target=`uname -m` kernel-2.6.spec 2> prep-err.log | tee prep-out.log The build failed at the end: Processing files: kernel-xenU-devel-2.6.9-67.0.20.EL Checking

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