User: Inigo Martincorena

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Sanger Institute, Cambridge, UK
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imartincorena
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Posts by Inigo Martincorena

<prev • 7 results • page 1 of 1 • next >
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Not really, when calculating p-values for 20,000 genes, you expect many (~1,000) to have p-values<0.05 by chance. q-values are corrected for multiple testing to avoid this and so q-values should always be used. You can use a less conservative q-value cutoff (e.g. 0.10) but I would be careful as y ...
written 1 day ago by Inigo Martincorena100 • updated 1 day ago by RamRS20k
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Hello, The outputs that you are asking for are not standard outputs from dndscv. They can be obtained with some additional calculations based on the outputs of dNdScv and following the methods of [my paper in Cell][1]. However, the risk of these measures being misused or misinterpreted by users with ...
written 1 day ago by Inigo Martincorena100 • updated 1 day ago by RamRS20k
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... You can certainly try dNdScv, running it separately on each set of patients and on both sets together. This will give you lists of significant genes and some measure of selection. However, dNdScv is not designed to look for differences between two cohorts, so you may want to consider alternative app ...
written 6 days ago by Inigo Martincorena100
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... I would need to know more about your project to give you a good answer. It all depends on how clean your table of somatic mutations is. Many false positives and artefacts tend to have low allele frequencies, and filtering them out may improve the results. However, if your dataset is clean, you don't ...
written 6 days ago by Inigo Martincorena100
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Answer: A: How to pass MAF file to dNdScv to detect cancer driven genes?
... Hello, Yes, to run dNdScv you need to provide the mutations in a simple 5-column dataframe, with the following columns: sampleID, chromosome, position, reference base, mutant base. You can follow the example in the tutorial below: http://htmlpreview.github.io/?http://github.com/im3sanger/dndscv/blo ...
written 7 days ago by Inigo Martincorena100
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... **I think it is fine to dismiss those contigs to study selection and to search for cancer genes**. However, if you are very interested in including these contigs in the analysis, you can build your own RefCDS object using the buildref function in the package (see a tutorial below). But I would not w ...
written 7 days ago by Inigo Martincorena100
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Answer: A: dNdScv error: Zero coding substitutions found in this dataset
... Thanks for trying the dNdScv package and the feedback. I suspect that the problem is that your chromosome names are different to those used by dNdScv. Your chromosome names contain the prefix "chr", while the reference object used by dNdScv for GRCh37/hg19 does not use this. As a result, the method ...
written 7 days ago by Inigo Martincorena100

Latest awards to Inigo Martincorena

Scholar 7 days ago, created an answer that has been accepted. For A: dNdScv error: Zero coding substitutions found in this dataset
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: dNdScv error: Zero coding substitutions found in this dataset

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