Hello Qiime Forum Folk,
I'd like to ask for some help with determining otu co-occurrence. We have a set of 90 samples (3 dietary groups, 30 individuals per group). All are human faecal samples and we have around 3000 sequences/sample (FLX-titanium). I've passed the samples through the QIIME initial pipeline and we have alpha and beta diversity data that shows similarities and differences between the sample groups. Next we'd be interested to find out if any species (otu's) are more likely to be found together, regardless of sample or other metadata. The aim is to study cultured organisms in vitro, however the choice of species to study in co-culture is not trivial. We've got some ideas just by eyeballing the data but I noticed that the 'otu_category_significance.py' script should allow me to carry out co-occurrence analysis. I've looked through the script details and generated a couple of output files, but am confused as to how to read the results.
The script information states "The script can also be used to measure co-occurrence. For instance it can also be used with presence/absence or abundance data for a phylogenetic group (such as that determined with quantitative PCR) to determine if any OTUs co-occur with a taxon of interest, using the ANOVA, G test of Independence, or correlation."
So I've got an otu table, with abundance data and taxonomy information attached. How to I look for pairs of otu's that might be linked more frequently that expected by chance?
I was also thinking of trying the "make_otu_network.py" script. Again, whilst I can generate output files and look at these in Cytoscape I can' for the life of me work out how to look at otu - otu linkages (rather than sample - otu linkages).
My apologies if I'm missing something obvious (ie: being a bit dim). Any help would be much appreciated.
I'm currently running QIIME 1.4.0 (macqiime on a macbook pro laptop). print_qiime_config.py -t output is pasted below.
Many thanks,
Blair