SNRNS
commented
2 years ago Hi Birong,
Below my reply:
On Wed, Jan 19, 2022 at 6:13 AM Birong @.***> wrote:
Hi all,
Thanks for developing such a cool package!
I have tried using TCGA-BRCA data and it works great! But I have a small problem, what can I do if I want to use all TCGA PanCancer data? Do I need to run them one by one, like the commands below, or can I run them together? Or I should use other tools, like Cibersort or xCell?
I would run them per tumor type, because the signatures were generated in a way that they account explicitly for tumor type. The lines below look good to me.
In our paper, we show that ConsensusTME outperforms Cibersort (original version) and xCell, but of course, you are free to do a comparison yourself. If I were you I would try more recent tools and compare against them like CIBERSORTx (new version) and BayesPrism probably: https://github.com/Danko-Lab/TED
ConsensusTME::consensusTMEAnalysis(bulkExpMatrix, cancer = "BRCA", statMethod = "ssgsea") ConsensusTME::consensusTMEAnalysis(bulkExpMatrix, cancer = "OV", statMethod = "ssgsea") ...
If I need to run the different types of cancer data one by one, that means I get many files of immune cell results.
Yes
If I wanted to group and compare these immune cells by an indicator, do you think I could combine those results?
Yes
Is there any batch effect between these results?
We didn't see batch effects when using TCGA data. But you can also have a look yourself once you get the results. The reason I think there's. no batch effect in TCGA is because the data come from many different sources, hospitals, etc and there's no single consistent batch/artifact running into the data. If you were to do batch correction, I would do that at the level of RNA counts. But for TCGA I don't think people do this.
I don't know if I'm making myself clear, let me know if you need more details! Thanks.
Best regards, Birong
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BirongZhang
Hi all,
Thanks for developing such a cool package!
I have tried using TCGA-BRCA data and it works great! But I have a small problem, what can I do if I want to use all TCGA PanCancer data? Do I need to run them one by one, like the commands below, or can I run them together? Or I should use other tools, like Cibersort or xCell?
If I need to run the different types of cancer data one by one, that means I get many files of immune cell results. If I wanted to group and compare these immune cells by an indicator, do you think I could combine those results? Is there any batch effect between these results?
I don't know if I'm making myself clear, let me know if you need more details! Thanks.
Best regards, Birong