User: dsull
dsull • 420
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Posts by dsull
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... If you're unsure, the default options work well (and without any detailed description of your experiment or what you want to gain from it, we really can't recommend much anyway).
Anyhow, here's what I usually use.
First, generate the genome index:
```
STAR --runThreadN 8 --runMode genomeGenerate ...
written 1 day ago by
dsull • 420
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... Some ideas I have (others feel free to chime in).
Did your protocol use rRNA depletion or polyA enrichment? Is it possible that your library is contaminated? (there's typically always going to some degree of it, which could explain why you see some non-polyA-mRNA).
mRNA length doesn't matter -- it ...
written 5 days ago by
dsull • 420
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... I mean, yes, you can do GSEA for each tissue, and compare the enrichment results. ...
written 7 days ago by
dsull • 420
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... Yep! And the strata (rock layers) themselves can be dated by radioactive age dating (isotope half life decay). ...
written 8 days ago by
dsull • 420
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... To get time (in years), remember, in addition to mutation rate, we also have the fossil record.
Read into the concept of "molecular clock". ...
written 8 days ago by
dsull • 420
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... First thing to do is to make sure you downloaded the entire file (e.g. the file is not partially downloaded / corrupted). Check this by checking the md5 checksum of the files -- it should match the md5 sum the company provides you. Also, you can see if the size of the file that the company gives you ...
written 8 days ago by
dsull • 420
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... I agree with this. P values basically tell you about evidence against the null.
There's also power analysis: if you know what your statistical power is (which is non-trivial to estimate), you can have an idea of your chances of committing a false negative (type 2 error) -- thinking a gene is non-DE ...
written 8 days ago by
dsull • 420
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... Well, if you want to know what genes belong to a certain category, say Genotype 1, you can simply print them out via:
`print(Genotype1)`
If you want to quickly see something like: genes that belong to Genotype1 and Genotype3 but don't belong to Genotype2 and Genotype4, again, you can subset your d ...
written 8 days ago by
dsull • 420
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... Question is very vague. What do these numbers mean? What do you consider expressed? Is anything that is not NA considered expressed?
Take a look at the Venn function here:
https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/venn
It gives you an example on how to create Venn diag ...
written 8 days ago by
dsull • 420
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... If you don't want to lose "information about expression", don't do an overrepresentation analysis, rather do a GSEA analysis for GO terms, pathways, etc. In GSEA, you input a ranked list of genes (ranking your genes based on strength of differential expression). ...
written 8 days ago by
dsull • 420
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