Can I find common genes by comparing one disease's rna-seq dataset with another disease's microarray dataset?

Question

[Md. Al - Mustanjid]

I want to find out common gene between two diseases; one disease dataset is based on high throughput sequencing (rna-seq) and another disease dataset is based on array (microarray), in this case can I find out common gene between two diseases?. Also need confirmation for validity. If yes then how can I analyze?

Please help me out. Thanks in advance.

Answer 1

[ATpoint]

With only two datasets this will not be a reliable analysis since disease is confounded by platform, which means that genes you find significant in disease A can either be specific for the disease or specific for the platform, so maybe not significant in disease B because the probes of the array do not properly capture the gene. In your case take the top significant genes and then do whatever downstream analysis you have in mind. For a confident assessment of disease-specific genes you need way more datasets to capture the heterogeneity of the diseases while also accounting for study-specific biases. A meta-analysis would be what you need with a large sample size.

[Md. Al - Mustanjid]

Thank you for your valuable info. Here I want to know another thing. If I have a ran-seq data of disease A and also rna-seq for disease B on the same platform and If i extracted DEGs from both diseases and find common DEGs; is this analysis ok? or your suggestion is most appreciated. Thanks in advance.