Hello, I have data from RNA-seq as raw read counts from 3 replicates from control and 3 replicates from treatment. I have to calculate Pearson correlations (PCCs) among the genes after using usual normalization procedures. One of the important transcription factor which is important for the biological hypothesis does not have any reads mapped to it, except in one of the replicates.
The biologists want me to use the expression data from RT-PCR experiment for the particular TF for calculating the PCCs, while using raw read counts for other genes. Is this okay to do or is there any solution to this ? Thanks.