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!
1 answer
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.
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