Hi all
I did normalization process through RMA in R for my datasets with Affymetrix platform (HGU133plus2). But my problem is i am getting duplicate gene symbols with different expression values. What step can i do to get unique gene symbols. Please help me out.
There are a couple of possibilities. You could use one of the MBNI re-mapped cdf files (google the last four words to find their site), which collate all the probes into single probesets per gene. Then you will just have one value for each gene. An alternative is to use findLargest in the genefilter package which will automagically select the probesets with the biggest difference in a given comparison.
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version 2.3.6
Thanks for the response. But i am not able to run this particular package findLargest. Could you suggest me any more options to do it.
I recommeded a function called
findLargest, which you can find in the genefilter package.Thank you Sir for your response. I did try. I can run findLargest in genefilter package. One more doubt, suppose my datasets consists of more than 50000 genes. What maximum rnorm do i need to give?
stats <- rnorm(50000).
You are taking the example too literally. That's a fake example that is used simply to show how the function works, and isn't intended to be how you use it in the real world. Instead, look at the Arguments section of the help:
Arguments: gN: A vector of probe identifiers for the chip. testStat: A vector of test statistics, of the same length as 'gN' with the per probe test statistics. data: The character string identifying the chip.The testStat argument isn't a randomly generated set of numbers - it is a set of statistics that you generated when testing for differences between your groups, and the
findLargestfunction finds the largest of these statistics, for each Entrez Gene ID.Thank you for your valuable suggestion. I got it :-)