Salmon with Sleuth

Question

[koaeb]

Hi,

I used "sleuth_prep(s2c, extra_bootstrap_summary = TRUE) " to create sleuth object, and I got a list contains obs_norm_filt, obs_norm and obs_raw, each of them also contains a tpm value. I searched lots of files online but none explained what's the difference among those data frames, especially what's the differences of the tpm within each dataset? what normalization it used?

Thank you!

Answer 1

[dsull]

obs_norm_filt = Filtered and normalized values; obs_norm = Normalized values; obs_raw = Raw values

The normalization and filtering are described here: https://www.rdocumentation.org/packages/sleuth/versions/0.30.0/topics/sleuth_prep

For the raw TPM values, the sum of all the transcripts within a sample should equal 10^6.

[koaeb]

Hi dsull,

Thank you!