Is it possible to run CibersortX with a very small number of samples?
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3 months ago
Sam ▴ 270

I am trying to impute group expression profile in CibersortX for a condition with 3 samples. For that, I have reduced my signature matrix to two cell types only (t-cells + "other").

However, running CibersortX (in GEP mode) throws an error

Error: $ operator is invalid for atomic vectors
In addition: Warning message:
In mclapply(1:no_cores, res, mc.cores = no_cores, mc.set.seed = FALSE,  :
  all scheduled cores encountered errors in user code
Execution halted

Adding samples removes the error.

Has anyone encountered this and succeeded to bypass?

cibersortx • 379 views
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Hi - Did you solve this issue, I am having the same problem

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also running into this!

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