Dear All,
I have sets of environmental data as well as OTUs of NGS data which is to be analysed for ecology and diversity. I tried all the tutorials and papers which should work well when using the sample file. I can't analyse my imported data. Herewith, I enclosed the screenshots of my imported data into R. I installed the required packages,
ade4,
ggplot,
mass,
stats,
Phyloseq,
QIIME,
Mothur, etc.
I am expecting someone to help me in these aspects. I would be very much grateful if someone would be willing to help me.
with thanks and regards
Siva
Instead of screen shots, could you post the code that you tried to make work? Usually, in R the installation is fine, but the code needs refinement and that can easier be checked if you just paste your code here. Also, have a close look at the structure of your data - are they configured in the same way as in the examples, i.e. number columns are numbers and not character because of single entries being misinterpreted by R etc.? Therefore, what does str(yourdata) as opposed to str(example data) give?
Hi
I do not really understand what you mean by "analysing your data" as you might first have a question to be answered then try to analyse your data relatively to your question and hypotheses. This said, there is an obvious problem in your data importation according to your first screenschot as V5 is probably not this long concatenated chain of characters... Check your import code, and try the readxls function in the package gdata, carefully specifying separators and comma-types. Then str(data) to check if everything is OK. If not, you have probably made a mistake and R is probably not responsible ! :)
Good luck.
Hi, although you have not specified the nature of your problem, a good starting point would be to use the phyloseq vignette, available here on bioconductor: http://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html, and tutorials, available here: http://joey711.github.io/phyloseq/tutorials-index - if you have specific problems, please post the code and any errors here, as Susanne suggests.
Dear All,
Thanks for your responses. I am not well in statistics. I am very average guy. By interest i came to know about linux and R. I have my own data. I am unable to write codes for my own data. If any one is interested to teach me very much welcome. If so, It would be a fruitful opportunity for me. If you want my data I can send.
Dear Matthew,
Thanks for your consideration. Kindly give me your email id. Will send you my data.
With best regards
Siva
Dear Matthew,
Thanks for your consideration. Kindly give me your email id. Will send you my data.
my email: [email protected]
With best regards
Siva
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