User: mark.ziemann
mark.ziemann • 1.1k
- Reputation:
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- Status:
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- Location:
- Australia/Mebourne/Monash University
- Website:
- http://genomespot.blog...
- Twitter:
- @mdziemann
- Last seen:
- an hour ago
- Joined:
- 3 years, 7 months ago
- Email:
- m***********@gmail.com
I'm a researcher at Monash University in Melbourne. I use Next Generation Sequencing to study epigenetics in a range of human diseases.
Posts by mark.ziemann
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... > combine, then adjust.
>
> Fisher's method has certain assumptions about what the p-value is that
> will almost certainly be violated if you do multiple-testing
> correction first.
Originally posted by [Brent P][1]
[1]: https://www.biostars.org/p/84242/ ...
written 29 days ago by
mark.ziemann • 1.1k
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... Best to open a new question - I'm sure the community can help you with your request :) ...
written 4 months ago by
mark.ziemann • 1.1k
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... > 1) Are there any other recommended ways to try to determine which
> genes in a bacteria are "differentially expressed" in response to a
> treatment (here UV radiation)? Is RNA-sequencing the preferred way to
> do this? I am only asking because you stated that "most reads will map
> ...
written 7 months ago by
mark.ziemann • 1.1k
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... > 1) Is RNA-sequencing possible for bacteria?
Yes. Although most reads will map to the highly abundant rRNA. DESeq2 will work just fine.
> 2) Would methylation studies be of interest for these 3 different
> levels of UV radiation in a bacteria? What type of R package would be
> useful ...
written 7 months ago by
mark.ziemann • 1.1k
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... The methylKit documentation includes an example where methylation scores are calculated on tiles (1kbp) ...
written 11 months ago by
mark.ziemann • 1.1k
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Comment:
C: Cut-off for genesets in GSEA
... Oh OK, so you want to exclude gene sets with fewer than 10 or 15 members. They are just unreliable.
You shouldn't exclude gene sets because they have more than X members. This GSEA feature is puzzling to me. I set the larger threshold to something really large like 5000. You can count the number of ...
written 11 months ago by
mark.ziemann • 1.1k
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... You're correct in that it could just be short length or rRNA. It is relatively easy to check the following:
1. Screen rRNA content http://genomespot.blogspot.com.au/2015/08/screen-for-rrna-contamination-in-rna.html
2. Simulate cDNA reads of the different lengths and determine the proportion that ...
written 11 months ago by
mark.ziemann • 1.1k
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... You're correct in that it could just be short length or rRNA. It is relatively easy to check the following:
1. Screen rRNA content http://genomespot.blogspot.com.au/2015/08/screen-for-rrna-contamination-in-rna.html
2. Simulate cDNA reads of the different lengths and determine the proportion that ...
written 11 months ago by
mark.ziemann • 1.1k
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... some tips here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165320/
I have used methylkit and it appears to work well. http://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html ...
written 11 months ago by
mark.ziemann • 1.1k
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... 2 good options:
recount2 https://jhubiostatistics.shinyapps.io/recount/
ARCHS4 http://amp.pharm.mssm.edu/archs4/
Also many GEO series include count matrices although these are generated by various pipelines. ...
written 11 months ago by
mark.ziemann • 1.1k
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