Question: differently expressed genes
gravatar for maryak
10 months ago by
maryak10 wrote:

Is there any way to check that i have obtained the correct set of differently expressed genes?can i come to know about differently expressed genes by just looking at normalized data? i apologize if some one find my question naive.

rna-seq gene • 251 views
ADD COMMENTlink modified 10 months ago by kristoffer.vittingseerup2.3k • written 10 months ago by maryak10

It is unclear what you have done, which data you have and what you are looking for. Please elaborate.

ADD REPLYlink written 10 months ago by WouterDeCoster40k

i have htseq-count TCGA breast cancer data and i have done TMM normalization. basically i want to use machine learning algorithms for my analysis

ADD REPLYlink modified 10 months ago • written 10 months ago by maryak10

You can check by qPCR.

ADD REPLYlink written 10 months ago by grant.hovhannisyan1.7k
gravatar for kristoffer.vittingseerup
10 months ago by
European Union
kristoffer.vittingseerup2.3k wrote:

The short answer is no. The reason we are doing DE in the first place is to find those genes :-)

That said:

  • If you are using a well establised, well tested (benchmarked) tool - and your p-value distribution looks good (for more information on this take a look at this blog) there is a good chance you have a good set.
  • Please note that with datasets like TCGA breast cancer (or single cell data) you have so many samples that you have the power to detect very small changes. Therefore I would recomend to also use a cutoff on effect size (in this case the absolute log2FC). This can even be done in the statistical test (testing abs(log2FC) > x instead of the default abs(log2FC) > 0) in a number of tools.
  • Lastly you can as Grant suggest do validations - this can both be experimental such as qPCR or by analysing other similar datasets.

Cheers Kristoffer

ADD COMMENTlink written 10 months ago by kristoffer.vittingseerup2.3k
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