Open gwaybio opened 3 years ago
@hkhawar - can you add an experiment
label to this issue?
@gwaygenomics Its done
@sMyn42
let's clone the fork of your repo here: /home/ubuntu/efs/2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad/workspace/software
@hkhawar documents the location of the _dmso.csv
files for the five plates in #1
@sMyn42 - it looks like the whitened files are never written to disk (see this notebook). We will need them written to disk since we will be analyzing them downstream in various ways.
@gway @hkhawar Here's my plan for getting this done:
In addition, when writing the whitened files to disk as part of the plan, would it be best to edit the notebook that deals with whitening (in order to write the files to disk) in place or to make a copy and edit that?
@sMyn42 My suggestion is to edit existing notebook for your whitening strategy
Looks like a solid strategy @sMyn42 - so that I can confirm my understanding, the dotted lines in the above graph indicates that these UMAP figures exist already (the ones @hkhawar already implemented), correct?
Yes
On Thu, Sep 24, 2020 at 12:34 PM Greg Way notifications@github.com wrote:
Looks like a solid strategy @sMyn42 https://github.com/sMyn42 - so that I can confirm my understanding, the dotted lines in the above graph indicates that these exist already (the ones @hkhawar https://github.com/hkhawar already implemented), correct?
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@gwaygenomics @shntnu Have a look at the plots of harmony batch corrected data. Though all the plates are not aligned perfectly but if we plot well wise we do see there is no segregation of well profiles in Umap space as we do observe in ZCA whitened data
This is really cool! I guess inverse harmony just got wiped out by the decomposition of the UMAP, but that ZCA transformation picture is r/dataisbeautiful worthy.
The Harmony batch corrected version certainly looks promising. But I stick to my recommendation in https://github.com/broadinstitute/2020-06-01-Evidence-of-state-switching-in-single-cell-drug-response-Broad/issues/2#issuecomment-721870683 i.e. consider just one plate and do all the analysis within the plate (because it appears that the well-position effect may not be as strong as we thought).
In #2 @hkhawar applied whitening to try to correct for batch effects. This issue will track the experiment/analysis of applying Harmony to the same DMSO profiles in #2
@sMyn42 will apply Harmony to the single cell profiles in two distinct ways:
In both ways, we will use Harmony to adjust for the
well
andplate
level variation.Visualization
We will apply
umap
to both traditional and inverse Harmony and visualize the resulting coordinates.Batch effect detection
We will also apply
kBet
to the following data transformations.Analysis Output
By the end of the analysis, we will have the following (in addition to the results in #2 ):