Hi,

I look to help of assessNumberSignatures in SomaticSignature package

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assessNumberSignatures(m, nSigs, decomposition = nmfDecomposition, ..., nReplicates = 1)

According to manual nRplicates is:

nReplicates: How many replicates should be used for assing a single value of 'nSigs'?  For decomposition methods with random seeding, values greater than 1 are reasonable.

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I understood that values greater than 1 are reasonable but i would like to know if replicates means biological replicates. What if i have only one lung cancer, one colon caner and one breast cancer samples. What if i have 10 colon cancer samples from different patients?

Thank you very much.

Here, the term replicates refers to the number of times the goodness-of-fit statistic will be recomputed. If a decomposition method uses a random seeding, stable results will require more than one run. This does not relate to technical or biological replicates, as we may use it to describe experiments. I understand that using the word "replicate" can be misinterpreted here, and I will update the documentation soon, in order to make this distinction clearer. Thank you for bringing this to my attention. You can also have a look at section 4.4 of the vignette, which may help with understanding the meaning of the parameter.

I have updated the documentation of the assessNumberSignatures function to give a more detailed explanation of the nReplicates parameter. This is part in version 2.4.7 which will become available within the next days.