Closed:Batch effect removal on q-RT PCR microRNA expression data

Question

[ivna.ivankovic]

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.