Vignette 1 with CAF-S1 and S4 numbers aren't matching about icellnet HOT 6 CLOSED

Hello,
I would be happy to help but I need a bit of context/explanation of what you did and current issues to identify what is happening...

from icellnet.

from icellnet.

Hello,
I cannot see what you generated, it is not attached to the previous comment, can you upload the results ?

I think I partially figured out what is happening. This tutorial has been created with an oldest version of the ligand/receptor database, so the plots may not be up-to-date. This may affect the values of global communication scores (as we take into account more interactions) and distributions, although this vignette is restricted to cytokine communication, which did not evolve much in the last version of the database. But the balloon plot values should not be affected.

from icellnet.

CAF_barplot.pdf
CAF_heatmap_pvalue.pdf
CAF_network.pdf
CAF_balloonplot.pdf

My apologies, here are the files. Thank you again for your assistance.

from icellnet.

Thanks.
I think there is a problem when running the gene.scaling function. In the tutorial:
PC.data=gene.scaling(data = PC.data, n=18, db = transform)
and
CC.data= gene.scaling(data = data, n=4, db = db2)

Normally, after applying this function, the matrix values should be between 0 and 10 for each gene. Maximum values of each interaction is thus 100 in the balloon plot.
Can you check head(PC.data) and head(CC.data) after applying the gene.scaling function ?
Or maybe you have an error message or a warning at this step ?

I hope it helps, let me know!

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That helped, the line got commented out somehow where the scaling was applied, the numbers for the balloon plot are matching now. The bar plot and p-value plots still have some slight discrepancies, but not as major as they were before, likely for the reasons you mentioned above. Thank you.

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