I can't find anything through searching so this must be a pretty noob question but any comments are appreciated.
I want to display abundance in expression experiments in a common format regardless of the tool used for the analysis (i.e. EdgeR, DESeq).
We have chosen RPKM to represent abundance using the formula:
(number of reads/kb of exon)/mill mapped reads
When there are multiple replicates how are the runs combined?:
1) the total count from all of the replicates (and the sum of the mapped reads from all of the replicates).
2) the average count of the replicate counts (The sum of the average counts used for the number of mapped reads)
3) the base mean of the replicate counts (the sum of the base mean used as the of mapped reads)
Thanks,
Bill
I want to display abundance in expression experiments in a common format regardless of the tool used for the analysis (i.e. EdgeR, DESeq).
We have chosen RPKM to represent abundance using the formula:
(number of reads/kb of exon)/mill mapped reads
When there are multiple replicates how are the runs combined?:
1) the total count from all of the replicates (and the sum of the mapped reads from all of the replicates).
2) the average count of the replicate counts (The sum of the average counts used for the number of mapped reads)
3) the base mean of the replicate counts (the sum of the base mean used as the of mapped reads)
Thanks,
Bill
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