<NA> values in rse_tx.RData

Question

<NA> values in rse_tx.RData

Closed this issue 5 years ago · 9 comments

Hey

I've noticed that there are some transcripts that contain NA's in the assay count table. E.g. ENST00000622420.1 in DRP001055. In this case there are NA's for all four samples. In the GTEx data there are a total of 4.2 million NA's e.g. for transcript ENST00000604479.5, but here it's only for a subset of the samples.

Could you please verify that for me and let me know how to interpret this? I've been struggling with his for a few days now.

Thank you

Answer 1 · 2019-09-12T13:58:50.000Z

Hi @hwartmann,

This is basically the same as the second question in leekgroup/recount#18 that Jack Fu @JMF47 will answer.

Best,
Leo

Answer 2 · 2019-09-12T14:12:37.000Z

Hi @hwartmann, I have responded in the other thread. Brief recap here is that when read-lengths of samples differ, we have differing abilities to estimate transcript abundances.

Answer 3 · 2019-09-12T14:21:57.000Z

Thank you for getting back to me @JMF47

So what is your suggestion to deal with these transcripts? Can I set the NA's to zero or should I drop any transcripts containing a NA?

Answer 4 · 2019-09-12T14:24:23.000Z

What is your objective? I would recommend against setting NAs to 0. Whether or not you drop a transcript that contains any NAs depends on what you would like to do with the data.

Answer 5 · 2019-09-12T14:26:14.000Z

Will I run into the same issue if I work with recount2 gene or exon counts?

Answer 6 · 2019-09-12T14:27:32.000Z

I do not believe so, but @lcolladotor can chime in on the gene and exon count front.

Answer 7 · 2019-09-12T14:33:58.000Z

OK, thanks. But in any case, we do not really understand how what you described can result in NA. Could you maybe elaborate a bit more or point me to source that would explain this to us?

Answer 8 · 2019-09-12T14:41:59.000Z

https://www.biorxiv.org/content/biorxiv/early/2018/01/12/247346.full.pdf. Particularly, the estimation of the feature matrix, which calculates the expect number of counts falling into each exon/junction feature depending for a random read of a certain read-length.

Answer 9 · 2019-09-12T15:08:42.000Z

There are no NAs on the counts for the gene/exon RSE objects. The counting method is different for those than for the transcript ones. See https://f1000research.com/articles/6-1558/v1 for the gene/exon ones.