You can use log TPM values in Qlucore or you can directly import an aligned BAM file and select the TPM option for normalization.
There are some things to consider using TPM and that is: Being a relative abundance measure, TPM suffers from the same potential problems as total count normalisation, and thus may need additional between-sample normalisation (e.g., quantile normalisation). Moreover, RSEM is often used to estimate abundance of transcripts rather than genes. Since transcripts often overlap each other, reads can typically not be assigned with certainty to one specific transcript, and the transcript abundance estimates are more uncertain than gene abundance estimates. Common statistical analysis methods for gene counts do not take this uncertainty into account, and the effect of this uncertainty on downstream analysis is not yet well understood. |
