Hi List, I have two questions: 1) I have a chip which is the same feature as u133A, however have much less mm probes. When using pm or mm method, the matrices have the same dimension. I wonder, do the methods assume the number of probes for pm or mm are the sames by default? How do you determine pm or mm probes? 2) The cdf I am using is the same size as u133A(I wish I could contribute my cdf), I only read in 5 chips. However running into memory problem quickly. For example, I did a boxplot on 5 chips, it gave memory error (I allocated 1G) after 10mins of plotting. Could somebody give me some tips besides breaking down the files (since I only have 5 files)? Best regards -h [[alternate HTML version deleted]]

On Sat, 15 Mar 2003, Wang, Hui wrote: > 1) > > I have a chip which is the same feature as u133A, however have much less mm > probes. When using pm or mm method, the matrices have the same dimension. I > wonder, do the methods assume the number of probes for pm or mm are the > sames by default? How do you determine pm or mm probes? > Hi Hui, it depends on the CDF file (or CDF package) that you are using. If that says that there's are a one-to-one relationship between PMs and MMs, then the package will also behave so. It is fairly easy to calculate expression values ignoring the MM values. If you want to do more complex setups with varying arrangements of PMs and MMs (if that distinction is still meaningful...?) , you probably will want to dig into the code - have a start at the function express(), and have a look at the structure of the CDF environments. Best regards Wolfgang