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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

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 <-

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 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 Gi20Jun11 0.001217

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 ?zg?l Universit? Libre de Bruxelles

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 9,94 804 25,06 1476,833333 40,04 1540,561404 50,11 1575,166667 52,46 349,222222 54,92 1941,5 57,29 1053,507042 60,11 1535,1 70,04 2244,963303 79,97 1954,507042 100,31 2679,140625 >

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

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 summary.manova(m) :" residuals have rank" 24<501. What can it be the reason for this error

Hello, I have a data matrix consists of species as columns and sites as rows. N Chlamydiae Deferribacteres GN12 Hyd24-12 KSB1 PAUC34f SC4 SPAM Thermi WPS-2 ZB3 AD3 Elusimicrobia GAL15 ABY1_OD1 OP9 Fusobacteria HDBW-WB69 OP11 WS1 SR1 ZB2 AC1 OP3 OP8 NC10 NKB19 TM7 WS3 Gemmatimonadetes Lentisphaerae GN02 Armatimonadetes Tenericutes Spirochaetes Epsilonproteobacteria TM6 Acidobacteria Chlorobi