Question

What assays are distributed with Recount TX data

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k.vitting.seerup ▴ 120

@kvittingseerup-7956

Last seen 16 months ago

European Union

When downloading Recount2 tx-dataset (either via the R package or via their website) such as this dataset I get a RangedSummarizedExperiment which contain 4 assays:

assays(rse_tx)

"fragments"
"ses"
"scores"
"df"

Fragments are self-explanatory (counts from paired end data) - but what are the other 3 "assays".

In advance - thanks!

recount recount2 RangedSummarizedExperiment • 1.7k views

ADD COMMENT • link updated 5.3 years ago by Leonardo Collado Torres ★ 1.1k • written 6.1 years ago by k.vitting.seerup ▴ 120

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Hi there, "ses" is the standard errors of the fragments estimates, "scores" is score between 0 and 1 that dictates how uniquely identifiable each transcript is under the model we fit (0 being perfectly redundant, and 1 being perfectly unique). "df" is the degrees of freedom that particular transcript has in the linear model. Thanks!

ADD REPLY • link 6.1 years ago jmfu ▴ 10

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Thanks! You should have added that as an answer so I could mak it as solved :-)

ADD REPLY • link 6.1 years ago k.vitting.seerup ▴ 120

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Yup, please do so Jack! ^^ This info gets reflected at the top of the package page http://bioconductor.org/packages/release/bioc/html/recount.html

Thanks!

ADD REPLY • link 6.1 years ago Leonardo Collado Torres ★ 1.1k

score 2 · Answer 1 · 2019-09-03

Ansker by @jmfu:

Hi there,

* "ses" is the standard errors of the fragments estimates,
* "scores" is score between 0 and 1 that dictates how uniquely identifiable each transcript is under the model we fit (0 being perfectly redundant, and 1 being perfectly unique)
* "df" is the degrees of freedom that particular transcript has in the linear model.

Thanks!

(so we can close this question)