Question: Normalization of gene expression data
0
gravatar for bioinfonerd
10 weeks ago by
bioinfonerd10
bioinfonerd10 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?

Thanks

rna-seq • 267 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by bioinfonerd10

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

ADD REPLYlink written 10 weeks ago by bioinfonerd10

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 10 weeks ago by WouterDeCoster32k

Thanks that was really helpful!

ADD REPLYlink written 10 weeks ago by bioinfonerd10

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

ADD REPLYlink written 10 weeks ago by Kevin Blighe28k
2
gravatar for WouterDeCoster
10 weeks ago by
Belgium
WouterDeCoster32k 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 10 weeks ago by WouterDeCoster32k
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