User: Dario Strbenac
Dario Strbenac • 1.4k
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- Australia
- Last seen:
- 1 day, 4 hours ago
- Joined:
- 7 years, 12 months ago
- Email:
- d*************@sydney.edu.au
PhD student.
Posts by Dario Strbenac
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... The percentage of Successfully aligned fragments is low. It's usually about 80%, not 20%. Quality control of your FASTQ files may reveal some unexpected issues.
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written 8 days ago by
Dario Strbenac • 1.4k
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... I wouldn't say that it's the correct approach, but if you are creating a heatmap plot with binPlots, it is best to reduce the number of rows in the heatmap. Having one row for each transcript would make its appearance more complex than necessary. I think including TSS unsupported by reads also could ...
written 5 weeks ago by
Dario Strbenac • 1.4k
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... Try processing one sample using RSEM and look at a few genes in IGV to see if the transcript with the majority of assigned reads seems plausible. I'm not convinced of the assertion that there are not enough reads to identify the most highly expressed transcript for each gene.
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written 5 weeks ago by
Dario Strbenac • 1.4k
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Answer:
A: Splicing analysis with ASpli
... No, you shouldn't concatenate all of the samples belonging to a particular class. You can specify which class each sample belongs to by creating a targets data frame. ASpli also doesn't required paired samples, so there's no reason to force samples from the two classes to be paired somehow.
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written 6 weeks ago by
Dario Strbenac • 1.4k
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... I don't have a recommendation.
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written 9 weeks ago by
Dario Strbenac • 1.4k
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159
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... You should avoid using nucleR for your data analysis. The package depends on RangedData which has been "... has been discouraged in favour of GRanges or GRangesList objects since BioC 2.12, that is, since 2014.". Moreover, RangedData will be deprecated in April and probably removed entirely from IRa ...
written 9 weeks ago by
Dario Strbenac • 1.4k
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... Do you have an estimate of the normal fraction of the tumour samples from a clinician? If the fraction is about the same for all tumour samples, then it's best to do no normalisation. Fold changes would be under-estimated but would be in the correct order.
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written 10 weeks ago by
Dario Strbenac • 1.4k
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... naiveRandRUV outputs the dataset with numbers compressed around 0. It's just a characteristic of the method. I like to avoid using RUV unless the PCA or MDS plot indicates that it's necessary.
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written 3 months ago by
Dario Strbenac • 1.4k
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... No, the packages I mentioned don't output genes selected based on a multi-class criteria. You would need to write the function yourself. Of course, there are many classifiers you can use and different methods will give better classification performance for different datasets.
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written 5 months ago by
Dario Strbenac • 1.4k
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... No. It's also bad design that the developers implemented the cost value a constant. The optimal value would differ based on the input dataset. The algorithm basically does feature selection and inputs the chosen genes into to an SVM classifier. You can implement a similar analysis with ClassifyR or ...
written 5 months ago by
Dario Strbenac • 1.4k
Latest awards to Dario Strbenac
Popular Question
10 months ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Popular Question
10 months ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Popular Question
14 months ago,
created a question with more than 1,000 views.
For TranscriptDb of GENCODE Genes
Supporter
2.1 years ago,
voted at least 25 times.
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion
5.0 years ago,
created 100 posts.
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