Summarization probe ID to gene : FRMA
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Last seen 4.8 years ago

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 ?

summarization FRMA affy • 623 views
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@james-w-macdonald-5106
Last seen 19 minutes ago
United States

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.

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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.

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Thank you James W. MacDonald

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