User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.3k
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Australia
Last seen:
1 week, 2 days ago
Joined:
7 years, 1 month ago
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d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 178 results • page 1 of 18 • next >
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Most Efficient Application of Voom to Regularly Increasing Study
... What is the most efficient usage of voom in a scenario where more batches are arriving at some time in the future? If voom is applied to each batch individually, then, due to filtering of each count matrix on CPM, the resulting normalised value tables of each batch contain a different number of rows ...
limma voom batch effect correction written 5 weeks ago by Dario Strbenac1.3k • updated 5 weeks ago by Aaron Lun14k
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Comment: C: plotMDS Input Feature Filtering
... Certainly, I could. I wanted to see if there was an obvious batch effect before I applied batch effect correction, because I like to try and avoid between-sample normalisation if it's there's no clear difference. The first batch has 14 male and 4 female samples, whereas the second has 21 male and 21 ...
written 9 weeks ago by Dario Strbenac1.3k
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Comment: C: threshold to filter lowly expressed genes
... Indeed, after reading it again, I noticed that I interpreted it incorrectly. ...
written 9 weeks ago by Dario Strbenac1.3k
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Comment: C: threshold to filter lowly expressed genes
... I think that the current wording is confusing. The explanation states "This ensures that a gene will be retained if it is expressed in both the libraries belonging to any of the six groups.". I read this as the two samples will belong to the same class, whereas the filtering is independent of sample ...
written 9 weeks ago by Dario Strbenac1.3k
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plotMDS Input Feature Filtering
... When examining the most variable genes for a clinical cancer dataset generated as batches on different days, I notice that the genes are mainly ones located on the X and Y chromosomes such as XIST, UTY, and ZFY. Is it common practice to subset the matrix to remove these before making MDS plots, as t ...
edger exploratory data analysis written 9 weeks ago by Dario Strbenac1.3k • updated 9 weeks ago by Gordon Smyth30k
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Comment: C: Importing Gene Symbols with makeTxDbFromGFF
... Another solution is to read the file twice, once with makeTxDbFromGFF and a second time with import.gff3. Then, the matching of IDs is easy and doesn't miss those newly discovered genes which GENCODE has annotated with symbols. ...
written 9 weeks ago by Dario Strbenac1.3k
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Importing Gene Symbols with makeTxDbFromGFF
... I'd like to import the GENCODE Genes GFF3 file with its gene symbols. By using columns on the TxDb object, it is apparent that only the gene_id field is imported, which has entries such as ENSG00000000003.14.How can I also import the gene_name column, which has values like TSPAN6? ...
genomicfeatures gff3 written 9 weeks ago by Dario Strbenac1.3k • updated 9 weeks ago by Valerie Obenchain ♦♦ 6.1k
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Comment: C: TCGAbiolinks query error
... The software currently has some errors. Hopefully, the developers will fix it soon and your problem will be resolved. ...
written 3 months ago by Dario Strbenac1.3k
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Comment: C: Match Pattern Vector to Subject Vector
... Thanks for the suggestion. However,  AhoCorasickSearch  currently doesn't support mismatches nor indels. I doubt that it would be useful for many genomics applications. I notice that my question is basically the same as another recent question. It might be a common use case worth an optimised soluti ...
written 5 months ago by Dario Strbenac1.3k
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Match Pattern Vector to Subject Vector
... Given that vmatchPattern doesn't work with a vector as the pattern and vmatchPDict isn't implemented, are there alternatives in R that don't involve using short read mapping algorithms and building indexes? ...
biostrings biostings written 5 months ago by Dario Strbenac1.3k • updated 5 months ago by Martin Morgan ♦♦ 19k

Latest awards to Dario Strbenac

Popular Question 3 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 13 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 4.1 years ago, created 100 posts.

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