Question: Assesment of the number of signatures when using SomaticSignatures package
1
gravatar for arsala521
3.2 years ago by
arsala52110
arsala52110 wrote:

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

 

ADD COMMENTlink modified 3.2 years ago by Wolfgang Huber13k • written 3.2 years ago by arsala52110
Answer: Assesment of the number of signatures when using SomaticSignatures package
1
gravatar for Wolfgang Huber
3.2 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Have a look at the error message and perhaps you will note from it that 8 is larger than 4. Therefore, try with n_sigs=2:4.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Wolfgang Huber13k

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?

ADD REPLYlink written 3.2 years ago by arsala52110
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