Dear group, I have a data frame with 180 rows and 25 coloumns (data from a affy experiment). I have 10 normals and 15 cancer lines. of 180 I have some duplicate gene names (arising from two different probesets for a single gene). I want to calculate the median expression value for these two identical genes. here I have 6 samples and 2 genes. gids N1 N2 N3 T1 T2 T3 T4 G1 10 12 11 40 46 39 46 G1 8 10 8 35 46 32 53 could any one please help me How can I calculate the median expression for these two identical genes. After I do this, I want to do clustering. thank you. srini

I am assuming that you want to "average" the gene profiles. See if this works: colMedians <- function(mat) apply(mat, 2, median) sapply( split( df, gids ), colMedians ) This is computationally inefficient as the number of rows increase but this should be reasonably fast for 180 rows. Regards, Adai Srinivas Iyyer wrote: > Dear group, > I have a data frame with 180 rows and 25 coloumns > (data from a affy experiment). I have 10 normals and > 15 cancer lines. > > of 180 I have some duplicate gene names (arising from > two different probesets for a single gene). > > I want to calculate the median expression value for > these two identical genes. > > here I have 6 samples and 2 genes. > gids N1 N2 N3 T1 T2 T3 T4 > G1 10 12 11 40 46 39 46 > G1 8 10 8 35 46 32 53 > > could any one please help me How can I calculate the > median expression for these two identical genes. > After I do this, I want to do clustering. > > thank you. > > srini > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >