Hi, I am using R and tried to normalize the data within each sample group using RMA. When I tried to import the all the normalized expression data as a single text file and make a boxplot, it showed discrepancy among the sample groups. I tried to scale them or re-normalize them again, so that it can be used for further analysis. Unfortunately, I did not manage it on using AffyPLM package. Would you please help me out with this problem. Thanks in advance. Best regards, H. Nawaz -- View this message in context: http://r.789695.n4.nabble.com/scaling-on-normlized-data-set-tp2996771p2996771.html Sent from the R help mailing list archive at Nabble.com.
hosnaw <hmnawaz <at> gmail.com> writes:> I am using R and tried to normalize the data within each sample group using > RMA. When I tried to import the all the normalized expression data as a > single text file and make a boxplot, it showed discrepancy among the sample > groups. I tried to scale them or re-normalize them again, so that it can be > used for further analysis. Unfortunately, I did not manage it on using > AffyPLM package. Would you please help me out with this problem.I suggest you try your question on the Bioconductor mailing lists; I suspect you'll have a better chance of an answer there. It would also be helpful to provide a reproducible example, and more detail about what 'I did not manage it' means. good luck Ben Bolker