bin-chen-lab / rges Goto Github PK

Hi all,

Thanks so much for sharing the drug repurposing scripts.

I am interested in cmap_signatures.RData in the RGES/RGES_IC50_CMap_data.R: script:

Then I tried to download both example_data and data from https://www.synapse.org/#!Synapse:syn6182429/files/, but there is no data named cmap_signatures.RData, and no folder named cmap.

Sorry for raising this issue, I know this code has been out for a long time. Any advice would be appreciated.

Thanks,
Birong

Hi all,
Thanks so much for sharing the scripts of RGES paper.
I have a question about this method. In detail, you use α|β|γ to adjust the RGES in target condition to reference condition, the α|β|γ were calculated as the mean 'difference value' between reference and target conditions grouped by different dose and time bin, however, if this method neglects whether the correlation between the drug signature and disease signature is POS or NEG, for example:
The RGES of drug A under 5uM and 6h is '3', and '10' under 10uM and 24h, the diff between them is 7; while drug B under 5uM and 6h is '-3', and '-10' under 10uM and 24h, the diff between them is '-7', the mean diff of these two drugs is '0'. However, it seems that is't not appropriate to use '0' to adjust all other drugs. I'm wondering if you have considered this or if I misunderstood this method.
It will be very appreciated that if you could help answer these questions, thank you!