User: Brian Gudenas

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Clemson
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Posts by Brian Gudenas

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biomaRt inconsistent errors with hsapiens_gene_ensembl
... Hello, Has anyone else been getting inconsistent errors when using biomaRt with the hspaiens_gene_ensembl dataset? for example:   mart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl") will give the following error  Error in useDataset(mart = mart, dataset = dataset, verbose ...
biomart written 4 months ago by Brian Gudenas0
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Comment: C: RUVg with differential transcript expression?
... Thanks for your help Davide, just wanted to post a quick follow-up if this may help others. I checked the p-value distributions and  sleuth + RUVg does appear uniform with a spike a 0, so it does appear to work.  I also tried your second approach, solely including the protocol as a covariate, simila ...
written 5 months ago by Brian Gudenas0
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RUVg with differential transcript expression?
... Hello all, I am curious if the RUVg normalization method (ERCC spike in normalization) is applicable to transcript-level counts for differential transcript expression, I know RUVseq was developed for gene-level counts but it seems like it would still be OK for transcript level count analysis? My  ...
ruvseq sleuth written 5 months ago by Brian Gudenas0 • updated 5 months ago by davide risso730

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