Immunedeconv CIBERSORT

Question

[dy001]

Hello,

I'm doing some deconvolution analysis with Immunedeconv package embedded function for CIBERSORT deconvolution. The source code and LM22 has been extracted from CIBERSORT itself. However, I realised the results from Immunedeconv gives me P value 9999 and there is no parameter function to annotate desired permutation under immunedeconv (apart from array, absolute and absolute_method). The p value results also vary when I try to run using web server for CIBERSORT.

Any ideas why or able to reproduce the same results, but using local R server?

Thanks!

Answer 1

[Jeason]

The 9999 is the default set of p value in CIBERSORT, there may be something wrong in your data. You need to check it.

[dy001]

I doubt it is to do with the raw data of my dataset. I applied onto the CIBERSORT web and the p value output is not 9999.