[R] zigzag confidence interval in a plot

Dear All, When I plot the values and linear regression line for one data set, it is fine. But for another one I see zigzags, when I plot the confidence interval cd Depth CHAOsep12RNA 9,94804 25,06 1476,83 40,04 1540,561404 50,11 1575,17 52,46 349,22 54,92 1941,5

[R] MANOVA summary.manova(m) : residuals have rank

Dear All, I am trying to perform MANOVA. I have table with 504 columns(species) and 36 rows) with two grouping (season and location) Zx - Z[c(4:504)] Zxm - as.matrix(Z) m- manova(Zxm~Season*location, data=Z) when I do summary.aov, I get respond for each species but summary.manova

[R] vegan -varpart is bigger than 100% in total?

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

Re: [R] spearman correlation and p-value as a matrix

  0.08266317  # Otu00209    Otu00218 #1  NaN -0.12705141 #2  NaN -0.61522514 #3  NaN -0.89010286 #4  NaN  0.03036290 #5  NaN  0.08266317 A.K. - Original Message - From: Ozgul Inceoglu ozgul.inceo...@ulb.ac.be To: R help r-help@r-project.org Cc: Sent: Thursday, February 14

[R] spearman correlation and p-value as a matrix

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

Re: [R] spearman correlation and p-value as a matrix

-0.6546537 #Otu00105_ag1    NaN A.K. - Original Message - From: Ozgul Inceoglu ozgul.inceo...@ulb.ac.be To: r-help@r-project.org Cc: Sent: Wednesday, February 13, 2013 4:48 AM Subject: [R] spearman correlation and p-value as a matrix I have two data matrices that I want to make

[R] subsetting data file by intoducing a second file

Hello, I have a very data matrix and I have a file which has the names that I need to subset. However I cannot manage to subset the main file. ANy idea? bg - read.table (file.choose(), header=T, row.names) bg Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131

[R] plot significant spearman correlation

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

[R] ggplot zoomin

Dear All, I am plotting a graph in ggplot, I would like to magnify the values between 0-1 without losing data in the higher range. How can I do that? neither scale_y_continous nor coord_cartesian works. Thank you Özgül Université Libre de Bruxelles

[R] labdsv-indval Windows GUI front-end stopped working.

Dear All, I have a problem with indval command. Last week, I could run it on my pc without any problem. Today, I tried to run the command indval and it constantly gives the error windows GUI front-end had stopped working, and it shuts the program. I was using 2.14.2 and I even uploaded new