Dear List, We have performed a high-throughput rtPCR experiment for selected 120 genes on 2,000 human subjects using TaqMan platform. There are two batches/runs, and three housekeeping genes used across all plates/runs. However, since there are about 2,000 blood samples which were NOT drawn at the same time from individuals, and RNA were NOT extracted at the same time. In genome-wide microarray data which include all 20,000 human genes , we could apply comBat or PCA to adjust for hidden variables. However, in our rtPCR data, there are only 120 genes measured on 2,000 samples, can anybody advise us whether comBat or PCA method is still applicable here? If not, do you have any suggestions for controlling for the latent variables? Please keep in mind that >90% of these 120 genes are highly or moderately expressed in blood samples. Many thanks, Shirley

Dear List, We have performed a high-throughput rtPCR experiment for selected 120 genes on 2,000 human subjects using TaqMan platform. There are two batches/runs, and three housekeeping genes used across all plates/runs. However, since there are about 2,000 blood samples which were NOT drawn at the same time from individuals, and RNA were NOT extracted at the same time. In genome-wide microarray data which include all 20,000 human genes , we could apply comBat or PCA to adjust for hidden variables. However, in our rtPCR data, there are only 120 genes measured on 2,000 samples, can anybody advise us whether comBat or PCA method is still applicable here? If not, do you have any suggestions for controlling for the latent variables? Please keep in mind that >90% of these 120 genes are highly or moderately expressed in blood samples. Many thanks, Shirley