Hi,

I have a question on qRT-PCR gene expression data analysis. I have a gene panel with 300 genes (292 test genes) + 8 housekeeping genes. The samples were run in batches over the period of time (first batch of samples = 90 + 3 Pooled Controls, Second batch = 50 + 3 Pooled Controls, Third batch = 70 + 3 Pooled Controls). Please let me know how should I normalize this type and handle batch effect.

Does the below approach makes sense?

• Combine the data (Ct values) from all the 3 batches (90 + 50 +70 samples) and save in *.csv file.
• Calculate Delta Ct = Difference between the Gene of interest and Arithmetic Mean of 8 housekeeping genes or Negative Delta Ct Ct(reference genes)- Ct(gene of interest).
• Plot PCA, heatmap etc.

Thank you,

Toufiq