User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.4k
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Australia
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d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 202 results • page 2 of 21 • next >
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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. ...
written 3 months ago by Dario Strbenac1.4k
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Comment: C: No BAM option in readAligned from the ShortRead package
... I don't have a recommendation. ...
written 4 months ago by Dario Strbenac1.4k
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Answer: A: No BAM option in readAligned from the ShortRead package
... 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 4 months ago by Dario Strbenac1.4k
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Comment: C: Normalise counts when tumour samples have normal tissue contamination.
... 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. ...
written 4 months ago by Dario Strbenac1.4k
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Answer: A: RUVnormalize- How to output a corrected expression matrix without negative value
... 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. ...
written 5 months ago by Dario Strbenac1.4k
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Comment: C: Changing SVM-Kernal in geNetClassifier function
... 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.   ...
written 7 months ago by Dario Strbenac1.4k
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Answer: A: Changing SVM-Kernal in geNetClassifier function
... 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 7 months ago by Dario Strbenac1.4k
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Comment: C: Differential gene expression of longitudinal data
... Is the second visit for every patient qualitatively the same? Why do some patients have three or more visits? ...
written 7 months ago by Dario Strbenac1.4k
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Reproducibility of MultiDataSet Comparison
... In the journal article explaining MultiDataSet, it is claimed that MultiDataSet is better than the competing MultiAssayExperiment because "... MultiAssayExperiment is being developed by a large number of contributors making package improvements (to MultiAssayExperiment) slow and tedious." I wrote to ...
multidataset multiassayexperiment written 9 months ago by Dario Strbenac1.4k • updated 9 months ago by Levi Waldron490
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Comment: C: Why does total unique map not equal to library size?
... Neither STAR nor HTSeq are Bioconductor software. Biostars is a more relevant forum. ...
written 9 months ago by Dario Strbenac1.4k

Latest awards to Dario Strbenac

Popular Question 6 weeks ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Scholar 6 weeks ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: how to extract read alignments from reads aligning in mulitple locations
Popular Question 12 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Scholar 12 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 12 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 12 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 16 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 2.2 years ago, voted at least 25 times.
Scholar 2.6 years ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 5.2 years ago, created 100 posts.

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