Question: Salmon with Sleuth
0
gravatar for koaeb
11 days ago by
koaeb10
koaeb10 wrote:

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!

rna-seq salmon sleuth • 110 views
ADD COMMENTlink modified 11 days ago by dsull1.5k • written 11 days ago by koaeb10
2
gravatar for dsull
11 days ago by
dsull1.5k
UCLA
dsull1.5k wrote:

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.

ADD COMMENTlink written 11 days ago by dsull1.5k

Hi dsull,

Thank you!

ADD REPLYlink written 8 days ago by koaeb10
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