Question: differently expressed genes
gravatar for maryak
4 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 • 186 views
ADD COMMENTlink modified 4 months ago by kristoffer.vittingseerup1.6k • written 4 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 4 months ago by WouterDeCoster37k

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 4 months ago • written 4 months ago by maryak10

You can check by qPCR.

ADD REPLYlink written 4 months ago by grant.hovhannisyan1.4k
gravatar for kristoffer.vittingseerup
4 months ago by
European Union
kristoffer.vittingseerup1.6k 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 4 months ago by kristoffer.vittingseerup1.6k
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