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batch effects

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Diane1

Participant

Posts: 7

Joined: Thu Jun 08, 2017 9:55 pm

Post Mon Nov 05, 2018 4:29 am

batch effects

Hello! I was curious to know how CyTOF users have been diagnosing and addressing possible batch effects (i.e, variation in data in a certain set of acquisitions). In this context, I also seek input on (i) lyophilizing CyTOF antibody mix in aliquots, (ii) known immune markers as internal controls.

Thanks for any help,
Diane
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AndrewD

Participant

Posts: 10

Joined: Tue Feb 20, 2018 7:18 pm

Post Mon Nov 12, 2018 12:24 pm

Re: batch effects

To address any type of batch effects you will need a control sample that is repeatedly stained in each batch. Alternatively you can retrospectively take a sample from each batch and stain/run them all in one set of aquisitions; this will hopefully inform you of relative staining differences between your original batches.

As you mention, you can reduce batch effects by mixing, aliquoting and freezing antibodies at the start of your project - effects of freezing on the staining efficiency of your panel needs to be tested. We have tried lyophilisation but have found it damages our antibodies so I would be interested in a protocol from someone who has successfully got this to work.

HTH
Andrew

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