User: piyushjo
piyushjo • 110
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Posts by piyushjo
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... Hi Kevin. Thanks for your response.
I did see that particular thread and the cited paper. However, I didn't understand how to apply the suggested formula to RNA-expression.
> qnorm((rank(x,na.last="keep")-0.5)/sum(!is.na(x)))
For example, what is X? Gene expression value or gene name, and what ...
written 24 days ago by
piyushjo • 110
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... Hi,
I just found out this new term "inverse normalized gene expression". I am reading a [paper][1] where they use inverse normalized expression instead of rpkm or vst normalized data for cox regression. Below is the statement from the publication.
> It is common to find extreme outliers in larg ...
written 25 days ago by
piyushjo • 110
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... Instead of UCSC browser you should try Ensembl Biomart. You can get mRNA sequence of each transcript of a gene.
For few genes you can use their [browser][1], for larger gene list you can use [R library][2].
[1]: https://www.ensembl.org/biomart
[2]: https://bioconductor.org/packages/release/bio ...
written 4 weeks ago by
piyushjo • 110
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... Hi JTA,
Nice to see another person looking for lncRNA in brain. I can share some resources I am aware of.
http://www.brainspan.org/
http://www.cdtdb.neuroinf.jp/CDT/Top.jsp
Read these papers
http://www.jneurosci.org/content/38/10/2399
https://genome.cshlp.org/content/28/8/1097.full
https://w ...
written 7 weeks ago by
piyushjo • 110
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... Ok. Thanks. I am comparing cerebellum to medulloblastoma (cancer of cerebellum). The only thing I think bothers me is if the anti-sense transcripts for an overlapping mRNA would be improperly quantified. ...
written 8 weeks ago by
piyushjo • 110
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... But main question is just because one library is stranded and the other is unstranded, would that make them incomparable? I understand differences from human and machines are also involved. ...
written 8 weeks ago by
piyushjo • 110
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... But doesn't DESeq2 takes into account the difference in library depth? What else could be contributing to variation?
...
written 8 weeks ago by
piyushjo • 110
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... Hi,
I have two datasets from different sources. Unfortunately one group have done unstranded RNA-seq while the second one has done stranded. When I do the PCA analysis of normalized reads using DESeq2, I see them clustering far from each other. Now I am doubtful if there is an artefact coming from ...
written 8 weeks ago by
piyushjo • 110
• updated
8 weeks ago by
johnsonnathant • 80
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... Hi Fuyingxue,
Thanks for your input and sharing the review article. ...
written 9 weeks ago by
piyushjo • 110
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... Sorry! I used the imagedb website. ...
written 11 weeks ago by
piyushjo • 110
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