Question: gene expression data analysis and batch effect methods
gravatar for Shamim Sarhadi
3.3 years ago by
Shamim Sarhadi210 wrote:

I have a gene expression data including intrinsic subtypes of breast cancer, but it does not have paired normal samples, Is it possible to use normal samples from different batch if I use batch effect removal methods eg COMBAT or DWD?

ADD COMMENTlink modified 3.3 years ago by WouterDeCoster44k • written 3.3 years ago by Shamim Sarhadi210

Hello Shamim Sarhadi!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k
gravatar for WouterDeCoster
3.3 years ago by
WouterDeCoster44k wrote:

No, that's not possible.
Your batch effect removal method doesn't know what is "technical-batch" difference and biological difference.

So when comparing tumor samples from batch A with normal samples from batch B you might be comparing technical differences in batch A with technical difference in batch B. Not biological differences. You don't know how big the batch effect is.

If you would have 4 tumor and 4 normal samples in batch A and 3 tumor and 3 normal in batch B you could combine the data and attempt batch removal, because now your software 'knows' which differences are biological and which are technical.

ADD COMMENTlink written 3.3 years ago by WouterDeCoster44k

Thank you WouterDeCoster Regards

ADD REPLYlink written 3.3 years ago by Shamim Sarhadi210
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