multi platform GEO analysis based in expression of one gene
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4 months ago

Hi there I have a challenge in analyzing GSE34941( It has 4 platforms) according to the expression of a specific gene in R. First, which is the best way to group my patients according to the expression of a gene to high- and low-expression? Second, which is the best way to remove the batch effect of multi-platform analysis here?

I really appreciate any help you can provide.

geo analysis microarray analysis geo R • 167 views
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In fact there are four platforms but these are all different experiments. There is the microarray-based gene expression profiling, then the bisulfite methylation analysis, and then the ChIP-seq (actually two "platforms" because they used both HiSeq and GAIIX). ChIP-seq is NGS; the other two are arrays, but as you talk about gene expression you should only use the array-based gene expression profiling, so there is no technical batch effect, at least not in the way you were probably assuming in the first place.

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Thank you so much. I don't know why I didn't pay attention to the experiment design of that GSE! Can you help me with GSE12417? How can I group my patients according to the expression of a gene to high- and low-expression? Also, which is the best way to remove the batch effect of multi-platform analysis?

I will be grateful for any help you can provide.

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Also, which is the best way to remove the batch effect of multi-platform analysis?

Please see my comment? There is no multi-platform experiment here in this case. There seems to be only one platform for the gene expression profiling.

How can I group my patients according to the expression of a gene to high- and low-expression?

You probably need some basic R couse, check the order function and get familiar with packages such as limma for microarrays.

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Hello amirnavidinia2014!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/15381/

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

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