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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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sQTL mapping: how to deal with 0/0 #8

Closed boxiangliu closed 8 years ago

boxiangliu commented 8 years ago

Hi David,

Thanks for making leafcutter available. I am wondering what your strategy is to deal with 0/0 in sQTL mapping. I have a few thoughts but none are quite optimal. The first one is to simply through these samples out (for the particular introns). However, neither matrix eQTL or fastqtl will be happy with missing data. Another thought is to consider them zero. However this perhaps does not reflect what is really going on. The final thought is to maybe use Laplace smoothing, making the proportion 1/N where N is the total number of introns in the cluster. The last one makes the most sense to me.

Do you have any thoughts on this?

Bosh

davidaknowles commented 8 years ago

Hi Bosh - I agree that statistically the correct thing to do is to exclude that observation (that's what the Dirichlet-multinomial would do implicitly). Yang maybe you can comment on how you did this with matrixEQTL?

On 28 June 2016 at 11:17, Boxiang Liu notifications@github.com wrote:

Hi David,

Thanks for making leafcutter available. I am wondering what your strategy is to deal with 0/0 in sQTL mapping. I have a few thoughts but none are quite optimal. The first one is to simply through these samples out (for the particular intron). However, neither matrix eQTL or fastqtl will be happy with missing data. Another thought is to consider them zero. However this perhaps does not reflect what is really going on. The final thought is to maybe use Laplace smoothing, making the proportion 1/N where N is the total number of introns in the cluster.

Do you have any thoughts on this?

Bosh

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/davidaknowles/leafcutter/issues/8, or mute the thread https://github.com/notifications/unsubscribe/AET_Bhz4BHzEHNHD9BF-OfcveEXqSKqrks5qQWVLgaJpZM4JAYjS .

David A. Knowles, Stanford University. E-mail: knowles84@gmail.com Web: http://cs.stanford.edu/~davidknowles/

goldenflaw commented 8 years ago

You can try setting the value to the mean/median if not too many are missing.

Yang

On Tue, Jun 28, 2016 at 11:21 AM, davidaknowles notifications@github.com wrote:

Hi Bosh - I agree that statistically the correct thing to do is to exclude that observation (that's what the Dirichlet-multinomial would do implicitly). Yang maybe you can comment on how you did this with matrixEQTL?

On 28 June 2016 at 11:17, Boxiang Liu notifications@github.com wrote:

Hi David,

Thanks for making leafcutter available. I am wondering what your strategy is to deal with 0/0 in sQTL mapping. I have a few thoughts but none are quite optimal. The first one is to simply through these samples out (for the particular intron). However, neither matrix eQTL or fastqtl will be happy with missing data. Another thought is to consider them zero. However this perhaps does not reflect what is really going on. The final thought is to maybe use Laplace smoothing, making the proportion 1/N where N is the total number of introns in the cluster.

Do you have any thoughts on this?

Bosh

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/davidaknowles/leafcutter/issues/8, or mute the thread < https://github.com/notifications/unsubscribe/AET_Bhz4BHzEHNHD9BF-OfcveEXqSKqrks5qQWVLgaJpZM4JAYjS

.

David A. Knowles, Stanford University. E-mail: knowles84@gmail.com Web: http://cs.stanford.edu/~davidknowles/

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boxiangliu commented 8 years ago

That makes sense. Thank you!