The bioBakery help forum

Masslin2 raw output data

Hello Huttenhower lab,
I am using Masslin2 and found a couple of potential outliers in the significant output scatterplot. I would like to take a look at the raw data output and determine replot without those potential outliers to see their effects. In the default output results, the raw data is not here. I am just wondering how can I get the output data.
I am also looking more into the meaning of Y-axis, is there a publication I can be directed to?
Thank you very much!
Yike

Hi!

We have discussed also printing out the transformed and normalized data in the output directory. That has not yet been implemented in the newest version of the tool but is on our list. Thank you for the suggestion!

For now, you can still look for those outliers in your input data as, I believe, the y-axis of the plots is the raw (input) abundance data, not the transformed data-- making it relatively easy to search the microbe in questions data in R and remove anything above X abundance. Additionally, increasing your prevalence and or abundance filter can often help with outliers in the data.

Best,
Kelsey

1 Like

Thank you, Kelsey! .