is in qiime possible to perform a 2ways anova testing treatments and sampling time?

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Valentina Imparato

Nov 19, 2015, 12:33:02 PM11/19/15
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Hi there!

I have another doubts how to proceed with my analysis to test significance between the treatments I have and depending on time of the incubation.
I have split the otu tables according to treatments and time and tested individually by but I am wondering if there is any script that allows me to test the 2 factors together. 
let's say I would like to compute the significance on the abundance depending on the treatment but I have independent sampling along time scale.
so I would like also to know if the incubation time is affecting the variation.
there is a way how to test time series samples in Qiime?
in the table a little portion of my samples for you to see. 
let's say that 37-42 are triplicates of 1 treatment relative to 2 time points, 43-48 the control relative to 2 time points as well.
the complete set has 4 treatments and 3 time points.

I have the 1.8 version of qiime.

Thanks you folks for help.

all the best,


EXTRACT OF TABLE from summarize_taxa (trimming the rare otu)

Taxon VAL037 VAL038 VAL039 VAL040 VAL041 VAL042 VAL043 VAL044 VAL045 VAL046 VAL047 VAL048
Bacteria;Acidobacteria;Acidobacteria_Gp4;Gp4;Other;Other 462 640 639 504 900 753 1046 632 587 323 547 467
Bacteria;Acidobacteria;Acidobacteria_Gp6;Gp6;Other;Other 943 1058 1482 1452 1804 1399 1371 1019 806 600 952 966
Bacteria;Acidobacteria;Acidobacteria_Gp6;Other;Other;Other 241 249 359 364 471 318 345 199 231 125 221 254
Bacteria;Actinobacteria;Other;Other;Other;Other 193 282 255 411 431 275 166 212 97 164 243 189
Bacteria;Bacteroidetes;Bacteroidetes_incertae_sedis;Other;Other;Other 157 163 154 96 147 160 111 114 54 85 67 43

Jenya Kopylov

Nov 19, 2015, 10:15:57 PM11/19/15
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Hi Valentina,

After discussing with Tony, you may need to use R for this. This link may be helpful. You can convert the OTU table into a tab-delimited format using Excel.


Will Van Treuren

Nov 19, 2015, 10:27:48 PM11/19/15
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Hi Valentina, 

Too add to Jenya's post, you can do a version of this test in QIIME by manipulating your metadata.  What you need to do is create a metadata column in your mapping file that is the concatenation of the two fields you are interested in (so treatment and time based on your previous post). You can create a new column in your mapping file, and populate is with something like TREATMENT_TIME where TREATMENT is the value under the treatment metadata column, and TIME is the value under the sampling time column (an excel formula like =concatenate(A2, "_", B2) will do the trick). 

Once you have this column, you can run against it, and it will tell you if any treatments are different based on this grouping. It is not as good as a normal two way ANOVA because it won't give you the p-values for the individual factors or interactions, but it might be a start without having to go to R. 

Hope this helps,

Barvaz Sini

Nov 20, 2015, 12:47:05 AM11/20/15
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Can you also try to a bit more exactly what you are looking for? Are you looking for a difference between the 2 treatments in any single time point? or in the final outcome? or a trend? what type of effect are you looking for?

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