Comments (5)
from simpletidy_genecoex.
Yes, you can use the tool without using any bait genes at all. You can look at this version of the script: https://github.com/cxli233/SimpleTidy_GeneCoEx/blob/main/Scripts/SimpleTidy_GeneCoEx_no_bait.Rmd where I didn't use any bait genes.
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On Thu, Jun 6, 2024 at 9:00 AM Shuangyang Wu @.> wrote: Hi Chenxin, Thanks for the wonderful tools. I was wondering if we could use SimpleTidyGeneCoEx for the network construction without using bait genes, as we are focusing on the de novo key genes finding based on the co-exp network. Best, Shuangyang — Reply to this email directly, view it on GitHub <#6>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALLXJPBEXPQSHZWZ23QVH6TZGBMQFAVCNFSM6AAAAABI4WATJWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMZTQMRQGM2DONI . You are receiving this because you are subscribed to this thread.Message ID: @.>
-- Li
Many thanks!
from simpletidy_genecoex.
Hi Li,
I went through the pipeline and it worked well.
I have one question maybe because I missed something: is there any function in the pipeline to determine the correlations between module and phenotype? ie: the cor value between module 1 and root is 0.9?
Thanks.
Best,
Shuangyang
from simpletidy_genecoex.
from simpletidy_genecoex.
No, I don't have that. The closest thing is the mean standard expression level of modules at each sample type. For example, Module 1 has z score of 2 at root. You can access that information from the module-sample heatmap. Using the heatmap you can see which module is most highly expressed at which sample, which serves the purpose of module-phenotype correlation.
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On Sat, Jun 8, 2024 at 10:07 AM Shuangyang Wu @.> wrote: Hi Li, I went through the pipeline and it worked well. I have one question maybe because I missed something: is there any function in the pipeline to determine the correlations between module and phenotype? ie: the cor value between module 1 and root is 0.9? Thanks. Best, Shuangyang — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALLXJPDAYSOPLYOKGOF242DZGMFZLAVCNFSM6AAAAABI4WATJWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJWGA2TAMJXHE . You are receiving this because you modified the open/close state.Message ID: @.>
-- Li
Hi Li,
Thanks, that's all I want as I assume the quantitation method is close to the association.
Best,
Shuangyang
from simpletidy_genecoex.
Related Issues (4)
- line graph HOT 9
- Metadata for the script HOT 3
- Single cell data set implimentaion HOT 1
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from simpletidy_genecoex.