Question: Summarization probe ID to gene : FRMA
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3.1 years ago by

I am using fRMA to preprocess my affy dataset from  hgu133a2 platform and I am getting a dataset with 54k unique probe id's in the eSet format, but I need to have a dataset with unique gene symbol or ENTREZID , as you know in the frma output there are a lot of prob ids that map to a gene Id , how can I convert my 54k probes dataset to a dataset with unique geneID ?

affy frma summarization • 466 views
modified 3.1 years ago by James W. MacDonald51k • written 3.1 years ago by Shamim Sarhadi20
Answer: Summarization probe ID to gene : FRMA
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3.1 years ago by
United States
James W. MacDonald51k wrote:

You could summarize using the MBNI Entrez Gene re-mapped probesets and the hgu133a2hsentrezgfrmavecs frozen RMA vectors. Or you could use the genefilter package to subset to unique Entrez Gene IDs.

Thank you  James W. MacDonald

Please correct me if I'm wrong, using genefilter in this case just help us to remove redundant prob-id's or those that have not expressed from a pre-defined cut-off while here for summarization we need to do something like calculating mean of peopsets to converting prob-level values to gene level (st more than a simple mapping between IDs) I appreciate if clear me , I am new in this field

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It's not clear to me what you are asking, so I will give an answer that might be useful. The difference between methods is that the MBNI cdfs collect all the probes that unambiguously map to a given gene into a single probeset, so after summarization you only have one probeset per gene. The genefilter package takes all probesets that map to a particular gene and then picks one, based on a measure of variability between samples. In both cases you end up with just one probeset per gene, so you will have to decide which method is 'best' for your application.

Thank you James W. MacDonald

I think genefilter is better for my application. all the best