I downloaded the RNA-Seq dataset from the depository and took it for analysis.
For a tissue, sequencing was done 12 times and therefore had different sets of reads and normalized counts. Now for plotting a graph, we need a single value how to get a single normalized count value for a single gene from different sequencing data.
Whether can we do the average or sum of the CpM values of individual runs?
Kindly give me your suggestions on this.
Hi,
To evaluate the expression of genes, compute the average of the CpM values as well as the standard deviation. Less variation in the CpM values between the 12 sequencing samples is seen with smaller standard deviations.
If the analysis considers the sum of the CpM values across 12 tissues, it leads to an increase in the expression of genes, which is not correct.
Thank you Govindkumar Balagannavar, for clearing my query. It was really helpful.
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