TODO for paper #2: DPGP clustering analysis

[annashcherbina]

Same as we did for hets. Need to run the clustering analysis for DMSO as well.

[annashcherbina]

DPGP clustering analysis for peaks:

Order is:
Control earlyG1
Control lateG1
Control SG2M
DMSO earlyG1
DMSO lateG1
DMSO SG2M

DPGP clustering analysis for genes:

Order is:
Control earlyG1
Control lateG1
Control SG2M
DMSO earlyG1
DMSO lateG1
DMSO SG2M

[annashcherbina]

More organized version of clustering figures:
https://docs.google.com/presentation/d/11tsBKPbJ3LMEk1kYkqe2A_xl6FJFoUmooEcWJDWRf5s/edit#slide=id.g2a8f18cee3_0_560

[akundaje]

Anna, It doesnt make sense to use DPGP clustering across different disconnected time series. You can use it separately for control and separately for treatment but not as a concatenation. DPGP has an explicit notion of time. The control and treatment are not a continuous time series.

…

-Anshul.

On Sat, Nov 4, 2017 at 7:42 PM, annashcherbina ***@***.***> wrote: More organized version of clustering figures: <iframe src="https://docs.google.com/presentation/d/e/2PACX- 1vTnCBHOiPXMaoTu5hvfSxpDSxaKtWIzAhP4vADhAHhtogBChEovwXvA9qQG zW7EeM0EhY_axGnDSWCb/embed?start=false&loop=false&delayms=60000" frameborder="0" width="960" height="569" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true"></iframe> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAI7EfdL4H4NWWiuQ4O7KJ4s0KlNLBC2ks5szSCPgaJpZM4QNCPA> .

[annashcherbina]

Should we just stick with k-means clustering for DMSO analysis then?
Or should DPGP be done on the fold change of DMSO vs Control over time?
Really we mostly care about the DMSO vs Control effect, not the time effect within the DMSO samples or controls separately.

[akundaje]

Kmeans is fine

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On Nov 8, 2017 3:24 PM, "annashcherbina" ***@***.***> wrote: Should we just stick with k-means clustering for DMSO analysis then? Or should DPGP be done on the fold change of DMSO vs Control over time? Really we mostly care about the DMSO vs Control affect, not the time effect within the DMSO samples or controls separately? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAI7EcOm11w4UOjSLgiMvNMqIO-w-UWnks5s0jgQgaJpZM4QNCPA> .

[annashcherbina]

I think Sundari wants the DPGP -- I already sent her those figures, so is it valid if I re-run it on the fold change? I already have kmeans results as backup if needed.

[akundaje]

Dpgp cannot be used for disparate time series because it assumes contiguous temporal order across the samples as you provide them. So you should switch to kmeans.

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On Nov 8, 2017 3:45 PM, "annashcherbina" ***@***.***> wrote: I think Sundari wants the DPGP -- I already sent her those figures, so is it valid if I re-run it on the fold change? I already have kmeans results as backup if needed. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAI7EV_DyBC4ItGMAI8YzuGR2Q-o_Clyks5s0j0PgaJpZM4QNCPA> .

[annashcherbina]

Yes I know, that's why I suggested the fold change of DMSO vs control.
So the three timepoints would be
DMSO / Control in earlyG1
DMSO / Control in lateG1
DMSO / Control in SG2M

That is a single time series, so why would that be wrong?

We basically get the same results with the DPGP & the kmeans though: #7 so I can go with those, but I think the DPGP visualizations are better.

[akundaje]

Ah I see. I didn't realize that's what you meant. I thought you meant fold change relative to expected background for ATAC. Sure. That would be fine.

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On Nov 8, 2017 3:54 PM, "annashcherbina" ***@***.***> wrote: Yes I know, that's why I suggested the fold change of DMSO vs control. So the three timepoints would be DMSO / Control in earlyG1 DMSO / Control in lateG1 DMSO / Control in SG2M That is a single time series, so why would that be wrong? We basically get the same results with the DPGP & the kmeans though: #7 <#7> so I can go with those, but I think the DPGP visualizations are better. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#11 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAI7Ea4lF-KdnRbyt2c6Jn_BwmuFopNFks5s0j8egaJpZM4QNCPA> .