Biom upload

[gdawg100]

I am hoping to resolve what could be a simple issue.

I am processing Miseq data with mothur. I want to port a .shared file over to shiny-ps.

I created a .biom file using the .shared and .constaxonomy files. I tried uploading. The file actually appeared to upload, but then didn't show up in the "select dataset" window.

I learned that mothur's biom file is 0.9.1, so I figured out how to create a .tsv and then go from .tsv to biom 2.1 (json or hdf5, doesn't matter).

For my test I just used the OTU data with the taxonomies.

Again, it looks like the files upload. I can see the select dataset window gray for several seconds, but then nada. At Paul's suggestion, I tried importing the biom files using phyloseq in Rstudio. That resulted in an error: Error in validObject(.Object) :
invalid class “otu_table” object: superclass "vector_OR_factor" not defined in the environment of the object's class

Clearly something is amiss with the original file. Any suggestions?

[gdawg100]

Update: I solved the otu_table object problem. So I can import my biom files into phyloseq, but they still don't show up in the shiny-phyloseq select dataset window.

Any suggestions?

[spholmes]

The easiest way to do this is to save the phyloseq object and then to load the object (something.RData) from the shiny windown, be careful, depending on window size the choice is usually below where you think it is, Good luck Susan

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On Tue, Feb 28, 2017 at 9:37 PM, gdawg100 ***@***.***> wrote: Update: I solved the otu_table object problem. So I can import my biom files into phyloseq, but they still don't show up in the shiny-phyloseq select dataset window. Any suggestions? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#70 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJcvb6XY8F1cs5anlv6Kc4sBDTg04ISks5rhQQIgaJpZM4MN3qp> .

-- Susan Holmes Professor, Statistics and BioX John Henry Samter Fellow in Undergraduate Education Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

[gdawg100]

Hi Susan,

Thanks for the tip. I've been swamped and wasn't able to get back right away. I'm a novice pounding my way through, kind of line by line. I created .biom files and as indicated above got them into phyloseq. I then saved and made sure that I could load/open it and get back my original matrix and it looks good. I was originally worried that the format in mothur, sample x otu (rows x columns) would be an issue, but when the .biom file is created it appears to be transposed, because the object in phyloseq has the right format, otu x sample.

I can upload into shiny-phyloseq, at least based on the upload bar and the fact that the file name appears next to the browse option, but it still does not show up in the dataset window. I've tried resizing the window, using up/down keys to navigate, etc. No file.

Any other suggestions?

[gdawg100]

And just to be sure, I've checked to make certain the problem isn't a browser issue. Do you know of an accessible dummy or example .Rdata or .biom file that should work and can be used to troubleshoot further? This seems like such a great toolkit that somehow I've got to figure out where things are getting stuck.

cheers, gk