Entering edit mode
6 days ago
htchd
•
0
I have a gene expression data from RNAseq, and want to test if it match(or its similarity to) any existing gene expression profile in the public domain or any such data. What test should I use to check?
I know GSEA is used to test if an existing geneset(much smaller than the whole genome) is enriched in a gene expression data. But what I want to compare is the similarity of two gene expression datasets(both are genome size, so about 20,000 genes).
Qiagen is able to show this type of analysis (inside Ingenuity Pathway Analysis, IPA) where they can compare your list of genes to thousands of public datasets (which they have curated/analyzed) and produce a table of similar results in a tool they call
Analysis Match.While IPA requires a license Qiagen has a help page available that explains the scoring scheme, in case you want to check the method they use : https://qiagen.my.salesforce-sites.com/KnowledgeBase/articles/Knowledge/Analysis-Match#Signature
Thanks for your reply. Is there any R package for this type of analysis or searching?
There may be a R package that does this but keep in mind that in order to do this comparison you would need to download the raw data from such datasets and analyze them exactly as your own data before any comparisons can be made. Qiagen does this internally (why they charge a substantial license fee for Analysis match).
So essentially you have two count matrixesand want to compare? Or just two samples and want to assess similarity? I don't see much alternatives to correlation plots but this doesn't really give much insights.
Yes. I want to see if there's a statistical test for this
I asked two questions, so a "yes" is not informative.
Sorry, I thought they are the same. I have two gene expression profiles(each with one column of gene name, and another column of fold change or expression level) and want to get a similarity score.
Is it hard for you to list the number of samples and runs? If you cannot figure it out, at least you can show the number of files and their column names? It's impossible to answer your question since you are not even sure what you are asking for.