Scatter plots of data

[Jake Beal]

Following up on our discussion yesterday afternoon, I have made some scatter plots that let us inspect the samples for patterns.  These have various combinations of color and shape being determined by group, voltage, and sample.  I've also plotted some the focus on the inter- and intra-group variation by dropping strong-green and normalizing against the overall geo.mean for a class of sample, as well as some that eliminate the non-matched samples.

Key takeaways:

- The failure of the strong green sample leaps right out (it's the green in samples-by-type)

- While there is some pattern in a group's voltage effect on level, its certainly not dominating the group-to-group variation.

Thanks,

-Jake

[Ariel Haim Hecht]

Hi Jake,

Thanks! Would you be able to upload the spreadsheet with the values that are in these plots? I’d like to play around with a few different plots myself.

Thanks,

Ariel 

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<samples-by-group.png><samples-by-type.png><samples-by-voltage.png><samples-good-norm-by-group.png><samples-good-norm-by-voltage.png><samples-matched-good-norm-by-group.png><samples-matched-good-norm-by-voltage.png>

[Jake Beal]

It's not a spreadsheet, it's a 4-D array built by analyses/tasbe/overall_scatter.m

You should be able to execute it yourself using either Matlab (if you've got access to it) or Octave (its free software alternative).

Thanks,

-Jake

On Tue, Feb 28, 2017 at 12:27 PM, Ariel Haim Hecht <arih...@stanford.edu> wrote:

Hi Jake,

Thanks! Would you be able to upload the spreadsheet with the values that are in these plots? I’d like to play around with a few different plots myself.

Thanks,

Ariel 

On Feb 28, 2017, at 8:51 AM, Jake Beal <jake...@gmail.com> wrote:

Following up on our discussion yesterday afternoon, I have made some scatter plots that let us inspect the samples for patterns.  These have various combinations of color and shape being determined by group, voltage, and sample.  I've also plotted some the focus on the inter- and intra-group variation by dropping strong-green and normalizing against the overall geo.mean for a class of sample, as well as some that eliminate the non-matched samples.

Key takeaways:

- The failure of the strong green sample leaps right out (it's the green in samples-by-type)

- While there is some pattern in a group's voltage effect on level, its certainly not dominating the group-to-group variation.

Thanks,

-Jake

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<samples-by-group.png><samples-by-type.png><samples-by-voltage.png><samples-good-norm-by-group.png><samples-good-norm-by-voltage.png><samples-matched-good-norm-by-group.png><samples-matched-good-norm-by-voltage.png>

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[Ariel Haim Hecht]

Hi Jake,

Great, thanks.

Btw, forgot to send it yesterday, and thanks Dave for the plug, if anyone’s interested, this is the paper that we just published:

https://www.nist.gov/news-events/news/2017/02/start-codons-dna-and-rna-may-be-more-numerous-previously-thought

https://academic.oup.com/nar/article/2990259/Measurements-of-translation-initiation-from-all-64

-Ariel

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