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...present in a speardsheet. The values needs to be calculated for each gene across the samples (refer the example). And, it should be a simple thing, but I am unable to do it right now ! The example re the structure of the spreadsheet is - # Example: MyFile <- read.csv( text= "Names,'Sample_1','Sample_2','Sample_3' Gene_1,87,77,88 Gene_2,98,22,34 Gene_3,33,43,33 Gene_4,78,,81 ", header=TRUE, row.names=1, as.is=TRUE, quote="'", na.strings="" ) And, I think this formula that can be used for z score is - (x-mean(x))/sd(x) And, apply() fun...

...00077464 C_068131 C_068131 OC_068131 - 2 00051728 C_044461 C_044461 OC_044461 - 3 00058738 C_050343 C_050343 OC_050343 - 4 00059239 C_050649 C_050649 OC_050649 - 5 00001761 C_000909 C_000909 OC_000909 - 6 00005119 C_002752 C_002752 OC_002752 - locs sample_1 sample_2 value_1 value_2 1 37316550-37317847 N C 1.9268400 36.77590 2 27058468-27060176 N C 0.1817890 5.58835 3 4761739-4763268 N C 0.2309000 7.54035 4 14565311-14567393 N...

Dear fellows, The two questions are on sm.density.compare(). I compare kernel density estimates of two arrays of data. I'd like to scale up y-axis so that I can show better the differences in y values. English is not my first language so I'll try to explain it. I would like to stretch y-axis a bit longer but not to change the range of y values. How can I do this? Second, I'm

...g the "FL_EARLY" average so that I no longer have any "gene_id" duplicates. Seems like this is a job for some version of the apply function, but searching and puzzling over this has not gotten me anywhere. Any help will be much appreciated! Example data: gene_id sample_1 sample_2 FL_EARLY FL_LATE 763938 Eucgr.A00054 fl_S1E fl_S1L 13.170800 22.2605 763979 Eucgr.A00101 fl_S1E fl_S1L 0.367960 14.1202 1273243 Eucgr.A00101 fl_S2 fl_S1L 0.356625 14.1202 764169 Eucgr.A00350 fl_S1E fl_S1L 7.381070 43.9275 1273433 Eucgr.A00350 fl_S2 fl...

...9;m looking at abundance p/m2 (hence decimals) vs environmental variables and have been using http://ecology.msu.montana.edu/labdsv/R/labs/lab12/lab12.html to guide me through. My organism data looks like this: Sample "Species_1" "Species_2" "Species_3" etc Sample_1 0 0.12432 0.3456 etc and is in a .csv file My environment data (.csv again) looks like this: Temp Water etc 18 33.3 etc I can get vegan to run the CCA with no problems but when I enter >cca1.plot <- plot(cca.1,choices=c(1,2)) I get the fol...