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compare data from different runs?

PostPosted: Thu Jul 05, 2018 7:49 pm
by nuonuo56924
Dear All,

I wanna run 40 human samples with CyTOF to analyze phospho signals. In order to do it, I decide to run 5 samples per time.
so, my question is--can I compare the data directly from different runs?

For example,
On 1st run, I got calculated raw value of median for CD68 is "218.42" of patient#1.
On 2nd run, I got calculated raw value of median for CD68 is "538.68" of patient#2.

Can I say patient#2 has higher level of CD68?

Thank you,
Ruru

Re: compare data from different runs?

PostPosted: Fri Jul 06, 2018 8:50 pm
by RuthCyTOF
Dear Ruru
When we do experiments over multiple runs we include a reference sample in each one of our samples. This is essential for normalizing across days and taking into account the variations of the technical side of the experiment. See Kleinsteuber et al or our editorial: Cytometry A. 2016 Oct;89(10):903-913. doi: 10.1002/cyto.a.22935 or https://doi.org/10.1002/cyto.a.22992.
Good luck!

Re: compare data from different runs?

PostPosted: Thu Jul 26, 2018 12:46 am
by nuonuo56924
Thank you Ruth. We already used beads to normalize our data. I do not know if the function of reference cells will be the same as beads.

Re: compare data from different runs?

PostPosted: Thu Jul 26, 2018 6:42 am
by Verhoeff
The beads are a way of normalizing the measurement in the machine itself. However the technical variation introduced during the staining and handling of the samples on different days is not accounted for then. Main one is the difference in staining cocktail conditions, i.e. the exact amount of cells, pipetting differences in amount of antibodies added. A reference sample in each batch has the same expression, so it can be used to normalize measurements across different stainings.

Jan