User: Francesc Castro

Reputation:
20
Status:
New User
Location:
Switzerland
Last seen:
16 hours ago
Joined:
4 years, 5 months ago
Email:
f***********@gmail.com

Posts by Francesc Castro

<prev • 7 results • page 1 of 1 • next >
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Answer: A: SomaticSignatures low mutation rates
... Thanks for the answer. Do you have a general estimation of the minimum number of mutations to have an reliable estimation of the signatures? I suppose that this number would be in function of the strength of the signature ...
written 4.4 years ago by Francesc Castro20
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SomaticSignatures low mutation rates
... Hi, I have a dataset of somatic mutations in multiple samples. Some samples have a really low mutation rates (~20 mutations) while others have more mutation burden (~2000 mutations). I understand that signatures estimation for low-mutation samples will be unreliable, but the inclusion of these samp ...
somaticsignatures written 4.4 years ago by Francesc Castro20
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Comment: C: SomaticSignatures nmfSignatures error
... Ok, I'll do it ...
written 4.4 years ago by Francesc Castro20
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Comment: C: SomaticSignatures nmfSignatures error
... I already expected that the estimated signatures for the low mutation samples would not be reliable, but do you think that the inclusion of these low-mutation samples would affect also to the definition of the different signatures?   ...
written 4.4 years ago by Francesc Castro20
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Comment: C: SomaticSignatures nmfSignatures error
... I have really low numbers for some of the samples. Below the link to the rda file containing both matrices, normalized and not normalized (vr_mm_trio_f) https://www.dropbox.com/s/n7fyyxljv2tbftq/motif_matrix.rda?dl=0 Thanks ...
written 4.4 years ago by Francesc Castro20
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Answer: A: SomaticSignatures nmfSignatures error
... You're right, problem solved. Sorry for the confusion with the previous version. You still want a have the motifMatrix with normalize = FALSE? Thanks a lot ...
written 4.4 years ago by Francesc Castro20
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SomaticSignatures nmfSignatures error
... Hi, I'm trying to run nmfSignatures function and I've got the following error > sigs_trio_nmf <- nmfSignatures(vr_mm_trio, n_sigs, nmfSignatures) Error in 1:r : NA/NaN argument Timing stopped at: 0.603 0.001 0.603 I suppose that this is caused because my matrix have some 0's. The example f ...
somaticsignatures written 4.4 years ago by Francesc Castro20

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