How to normalize OTU abundances in 16S-rDNA sequencing data by individual sample amount?

Question

[yuki.weber81]

I have extracted and sequenced 16S-rDNA from suspended biomass collected on filters. Now I want to divide the OTU counts by the volume of water filtered for each sample, in order to abtain semi-quantitative abundance estimates. Does anyone know a reasonalble way to do it? I'm using the mothur and phyloseq. Thus far I only found the option to normalize all samples to one value. In my case, however, I have different values (volumes of filtered water) for each sample.

Thanks for any suggestions,

Yuki.

[st.ph.n]

have you looked into QIIME?

[Asaf]

You can change the values of the counts matrix in the phyloseq object

Answer 1

[yuki.weber81]

Well, I also had a look at QIIME but since this is just a side project of my PhD I think I will stick with the mothur-SOP for now.

@ Asaf: Yes I was able to change the OTU table in the phylosec object. However I had to export, change, and re-import it. But it works! Thanks!