# Are RSEM expected counts log transformed?

**URL:** https://forum.depmap.org/t/are-rsem-expected-counts-log-transformed/1650
**Category:** Q&A
**Created:** [August 19, 2022, 7:19pm UTC](https://forum.depmap.org/t/are-rsem-expected-counts-log-transformed/1650 "2022-08-19T19:19:17Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![jkrushkal](https://avatars.discourse-cdn.com/v4/letter/j/87869e/32.png) [@jkrushkal](https://forum.depmap.org/u/jkrushkal)
#### Post date: [August 19, 2022, 7:19pm UTC](https://forum.depmap.org/t/are-rsem-expected-counts-log-transformed/1650/1 "2022-08-19T19:19:17Z")

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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?

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### Author: ![pmontgom](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/pmontgom/32/4_2.png) [@pmontgom](https://forum.depmap.org/u/pmontgom)
#### Post date: [August 31, 2022, 8:19pm UTC](https://forum.depmap.org/t/are-rsem-expected-counts-log-transformed/1650/2 "2022-08-31T20:19:15Z")

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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

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### Author: ![jkrushkal](https://avatars.discourse-cdn.com/v4/letter/j/87869e/32.png) [@jkrushkal](https://forum.depmap.org/u/jkrushkal)
#### Post date: [August 31, 2022, 8:34pm UTC](https://forum.depmap.org/t/are-rsem-expected-counts-log-transformed/1650/3 "2022-08-31T20:34:51Z")

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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