Second batch of lincs data

[gwaybio]

@shntnu - I remember you mentioning that we have another batch of Cell Painting data for this project. Can you point me to where this data lives?

We should work towards getting this data on here and processed. @sMyn42 is looking for a good dataset to test different batch effect correction tools (e.g. Harmony) to extend his Summer Research project. Having the second batch on here will help!

[shntnu]

The backends are at https://imaging-platform-cold.s3.us-east-1.amazonaws.com/imaging_analysis/2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad/plates/2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad_2017_12_05_Batch2_*_backend.tar.gz

Here's how you'd restore them
https://github.com/broadinstitute/imaging-backup-scripts/blob/master/glacier_restore.md

Here's the description of this data set
https://docs.google.com/document/d/1KA4j_grc1uxkCdhCzqEQSps8MGZf9NT7V_F8mmEwPGw/edit

[gwaybio]

PROJECT_NAME=2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad
BATCH_ID=2017_12_05_Batch2

[gwaybio]

list_of_plates.txt

[gwaybio]

batch 2 sqlite files now available internally at /home/ubuntu/bucket/projects/2015_10_05_DrugRepurposing_AravindSubramanian_GolubLab_Broad/workspace/backend/2017_12_05_Batch2

[gwaybio]

I added batch 2 data in #58 - We can also perform some sort of check, a quick dataset description, and add the results to https://github.com/broadinstitute/lincs-cell-painting/tree/master/comparison

[sMyn42]

Cool! I'm planning to get back at it this weekend.

…

On Mon, Feb 22, 2021 at 1:09 PM Greg Way ***@***.***> wrote: I added batch 2 data in #58 <#58> - We can also perform some sort of check, a quick dataset description, and add the results to https://github.com/broadinstitute/lincs-cell-painting/tree/master/comparison — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#57 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIPDAPY6RSSN7Y3NNQ4V4S3TAKMXFANCNFSM4V3WUEMQ> .

[gwaybio]

#58 only contains well profiles (levels 2-4b) - We also need to create consensus signatures (level 5) for batch 2 data

[gwaybio]

Creating batch 2 consensus signatures in #61

[gwaybio]

the second batch of LINCS data lacks several MOA/Target annotations in our existing metadata map.

We're troubleshooting this in #62 (comment)

[gwaybio]

I just started running the full profiling pipeline on both batches of data

[gwaybio]

full pipeline is complete, and now frozen, after merging #63