Are RSEM expected counts log transformed?

Q&A
1

Hello, were the two files with gene and transcript level RSEM expected counts log-transformed? The Q5/22 release provides the following information:
CCLE_RNAseq_transcripts.csv:
RNAseq transcript tpm data using RSEM. Log2 transformed, using a pseudo-count of 1

CCLE_RNAseq_reads.csv:
RNAseq read count data from RSEM.

Could you please clarify whether the values in these two files are the log2-transformed pseudo counts or original RSEM expected counts?

2

I believe the descriptions are accurate. The CCLE_RNAseq_transcripts.csv is described as being log2 transformed and CCLE_RNAseq_reads.csv are RSEM’s estimate of the read counts.

The two different files have different units.

Does that answer your question or were you asking something different?

Thanks,
Phil

3

Thank you very much for your response, it answered my question. After examining the files and re-reading the description, I also realized that CCLE_RNAseq_transcripts.csv has log2-transformed TPM values and CCLE_RNAseq_reads.csv has the RSEM output of read count values. Thank you for taking your time to respond, it was helpful to get your confirmation.

Julia