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3.2 years ago
amirnavidinia2014
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10
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.
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.
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.
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.
You probably need some basic R couse, check the
orderfunction and get familiar with packages such as limma for microarrays.Hello amirnavidinia2014!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/15381/
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