Question: Combining different conditions of study from different experiments (same platform) for microarray meta-analysis
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gravatar for devikaparvathy
7 months ago by
India
devikaparvathy20 wrote:

I would like to conduct a microarray meta-analysis of differential expression study of Condition1 vs Condition2 where I could not find many such specific studies with both Condition1 and Condition2 samples. However, there are various experiments that include either condition1 alone or condition2 alone from the same platform.

Could I just download the CEL files for Condition1 and Condition2 from two/three different experiments and process them as usual as a single experiment and identify the DEGs?

(Such an approach was used in https://academic.oup.com/nar/article/45/17/9860/4084660 - see Table 1/SCNvsWB)

However I would like to further make sure that the approach is accurate or Do I need to conduct any batch effect removal algorithms like ComBat before merging the two conditions for a single study?

ADD COMMENTlink modified 6 months ago by Kevin Blighe48k • written 7 months ago by devikaparvathy20
1
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe48k
Kevin Blighe48k wrote:

Difficult to give a conclusive answer. I would proceed to obtain all files and then process them assuming no batch effect. A PCA bi-plot will then quickly reveal any batch effect. May also see it on the box and whiskers plot. If there is a batch effect, you have 2 options:

  • directly modify your data to adjust for batch, e.g., via ComBat, SVA, removeBatchEffects (limma), etc
  • include batch as a covariate in your design formula

Kevin

ADD COMMENTlink modified 5 months ago • written 6 months ago by Kevin Blighe48k
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