Question: Normalization of gene expression data
gravatar for vidushi.kapoor.home
3 days ago by
vidushi.kapoor.home0 wrote:

Hi everyone,

I have 50 samples gene expression data and I normalized them together. Now I want to use just 20 samples out of these for my analysis, do I need to normalize the raw counts of these 20 samples again or I can use the normalized values from the normalization (50 samples norm) that I did before?


rna-seq • 164 views
ADD COMMENTlink modified 3 days ago • written 3 days ago by vidushi.kapoor.home0

Thanks a lot! Could you also let me know the advantages of doing that?

ADD REPLYlink written 3 days ago by vidushi.kapoor.home0

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Say that you have a few outliers in your samples. The result of these on the normalization will be bigger when you only have a few samples. When you have more the effect will be diluted.

ADD REPLYlink written 2 days ago by WouterDeCoster30k

Thanks that was really helpful!

ADD REPLYlink written 2 days ago by vidushi.kapoor.home0

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

ADD REPLYlink written 2 days ago by Kevin Blighe23k
gravatar for WouterDeCoster
3 days ago by
WouterDeCoster30k wrote:

If all samples were processed on the same platform/same kit/same lab the best normalization you can obtain is to include as many of them as possible, so in this case normalize using 50 samples and only use 20.

ADD COMMENTlink written 3 days ago by WouterDeCoster30k
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