Finding similarities of 2 independent samples
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2.4 years ago
bharata1803 ▴ 530

Hello,

So, I downloaded from 2 NCBI GEO dataset with same type, iPSC. Is it possible to compare whether these 2 samples of iPSC are the same or not? My goal is to find whether reprogrammed cell from same mature cell (fibroblast) produce same iPSC. What kind of method is possible? Thank you.

RNA-Seq • 449 views
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If I understood correctly, you want to check whether both of them have same gene expression profile or not. There are many ways to check this. One of the simplest way is to compare the log2(Normalised gene expression) through pairwise correlation (e.g Pearsons correlation). Normalised gene expression could be TPM, RPM, RPKM or FPKM. Correlation value range from -1 to 1. +ve correlation value suggest there is some relation between two samples. Correlation more than 0.9 generally considered as good correlation to claim they are quite similar.

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It depends on how you define "same". My understanding of the question would lead me to compare the gene expression levels of the two iPSC not their differential expression profiles relative to the starting cells. For this you would need to normalize the expression levels so that they are comparable. The normalization method to use would depend on the type of data.

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Well, same in the definition of gene expression. What I imagine is if I clustered the sample, I will be able to group them in the same category.

I understand this will be affected by sample normalization or sequencing variance. Is there any method to normalized this variance?

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Maybe this paper (and associated R package) can help you.

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