Hi,
I'm using RSEM to compute gene expression values for two different RNA-seq sample. RSEM outputs tau value which I then converted to TPM value by multiplying it by 10^6.
1) Is there a minimum cutoff value I should set for TPM value? I see some papers filter out genes with TPM < 1 or TPM < 5 before proceeding to further analysis. How do I determine what cutoff should be used?
2) In a set of gene expression results, is it possible to determine which genes are considered highly expressed and which are expressed at low levels? I've see some papers use 1 < TPM < 9 as low and TPM >=100 as moderate/highly expressed, while others use percentiles (e.g. >= 75% percentile as highly expressed).
Thanks in advance.
I'm using RSEM to compute gene expression values for two different RNA-seq sample. RSEM outputs tau value which I then converted to TPM value by multiplying it by 10^6.
1) Is there a minimum cutoff value I should set for TPM value? I see some papers filter out genes with TPM < 1 or TPM < 5 before proceeding to further analysis. How do I determine what cutoff should be used?
2) In a set of gene expression results, is it possible to determine which genes are considered highly expressed and which are expressed at low levels? I've see some papers use 1 < TPM < 9 as low and TPM >=100 as moderate/highly expressed, while others use percentiles (e.g. >= 75% percentile as highly expressed).
Thanks in advance.
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