Kaitlyn’s notebook: MetboAnalyst procedure

My datasheet needed to be manipulated before using MetboAnalyst (I assume I will need it organized this way for some other stats I will run in the future since MetboAnalyst uses R.) They have a helpful link for data formats.

I had to include all 3 silos because MetboAnalyst requires that each group (in my case each day) had to have 3 replicates. In this case my “replicates” will be each silo, but the replicates are considered different samples and thus they will be analyzed separately and not grouped.

Excel tips:

=RIGHT(A1,LEN(A1)-3) <– removes first three characters in a cell
=LEFT(A1,LEN(A1)-3) <– removes last three characters in a cell

  • Time-series + one experimental factor (samples in columns):

Data-organization-Metbo.PNG

MetboAnalyst

  • Upload your data.
    • Data type = spectral bins (no data type will match my data since this is made for mass spec files; I am only using it for statistical analysis)
    • Format = Samples in rows (unpaired)
  • Next:Unpaired-Data-Integrity-Check-Metbo
  • Step 2: I accepted the default settings for missing value estimation.

 

  • Step 3: SD because I’m most interest in the trends of abundance over time.
  • Step 4-Normalization: My data is already normalized so I didn’t select any options.4-no-normalization

    I don’t think these graphs matter since they are again looking knfor ms peaks, but here they are anyway.4-normalization-feature_view4-normalization-sample_view

  • Step 5: analyze. Here are the types of analyses you can do now! 5-analyses