I am comparing the expression of four miRNAs between 34 patients and 4 controls. The data are obtained by q-RT PCR, SYBR green method. Mean Ct values are used.
To increase the number of control samples I downloaded the dataset from EMBL-EBI Array Express database and I want to integrate 10 more controls to my dataset. In their experiment they used q-RT PCR but with Taqman method.
Any recommendations on how to correct for a batch effect would be extremely appreciated.
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written
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ivna.ivankovic •
1 answer
How were you planning to process the data? - you should be able to specify a formula for the purposes of deriving p-values and other test statistics, in which case you could include batch as a covariate in such a formula.
For example:
outcome ~ gene + batch
This can then be used with t.test(), aov(), lm(), glm(), etc. This has the effect of adjusting for the effects of batch.
You may also take a look at the qpcR package in R.
Even with 34 vs 14, it is still an unbalanced dataset.
Kevin
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