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arsala521
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@arsala521-10976
Last seen 7.8 years ago
Hello
I am analyzing data through SomaticSignatures package. I am trying to use assesNumberSignatures function to determine number of signatures.
I entered the following commands:
> n_sigs = 2:8
> gof_pca = assessNumberSignatures(cancer_mm, n_sigs, pcaDecomposition)
When I entered the second command, I got the following error:
Error in findSignatures(m, nSigs, decomposition, ...)
'nSigs|r' must be a single positive integer in the range [1,4]
Would someone please help me in this?
Regards
I did try with 2:4. I got the plot but I was bit confused in choosing the number of signatures from the given plot.
As number of signatures has to be chosen such that with increasing the number of signatures the RSS and the explained variance do not change sufficiently. When I plotted using n_sigs=2:4, the resulting plot showed that RSS and explained variance changed till number of signatures = 4. I was not able to judge from the graph that whether with increasing the number of signatures beyond 4, the RSS and explained variance would change or not.
How would I choose number of signatures in such case?