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data analysis from multiple runs

PostPosted: Thu Jul 26, 2018 12:43 am
by nuonuo56924
This is Ruru, who is a postdoc working in UI health.

We are using Cytof2 for phospho-signaling analysis. I are collecting human samples over this year and next year. So, every 2 weeks, we run a CYTOF for collected human samples. I am wondering how should I compare datas from multiple runs.
For example, on the 1st run,
I get data for sample #31, #34, #35, and #36. Shown as attached.

On the 2nd run, I get data for sample #28 and #33. Shown as attached.

The statistic table shows the calculated raw values of medians using X-Axis channel: Panel/Channel values.

The question is:
1. Can I combine these two datas from different runs (they have different Ir control and gating strategy.) by Cytobank?
2. Can I compare the expression levels from the statistic table directly between different runs?
For example:
I copied the data from two statistic tables into the excel. Shown as attached.
Can I say sample #28 (3.49) has lower expression level than #31(16.79)?

BTW, my data was already normalize by beads.

I am looking forward to your response!

Best regards,