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Batch effect adjustment using Housekeeping Genes

Hello, starting from a txt file with count data, I am analysing RNAseq data from three different independent  experiments which should be merged into a single analysis. Sample characteristics, such as disease conditions, are perfectly confounded within the batches. The use of housekeeping genes, such as those suggested by Eisenberg et al. (, could be one way of addressing the batch effects. Is there a way in JMP Genomics which allows specifying sets of genes which could be used to adjust the batches?

Thank you so much for your time.

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Re: Batch effect adjustment using Housekeeping Genes



In JMP Genomics, you can use Loess Normalization within Expression>Normalization to specify a control set or housekeeping set of genes for normalization.  See documentation here:


Hope this helps,



Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail:
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