[R] Normalization problem

2006-07-25 Thread Nayeem Quayum
At first I would like to express the gratitude toward Oosting, J. and James MacDonal for their help solving the previous problem I posted on this forum. Now I have a new problem. I was trying to normalize set of microarray data on HGU133 paltform. I put all the HGU133A platform chips in one

[R] Help regarding mas5 normalization

2005-11-10 Thread Nayeem Quayum
Hello everybody, I am trying to use mas5 to normalize some array data and using mas5 and mas5calls. But I received these warning message. If anybody can explain the problem I would really appreciate that. Thanks in advance. background correction: mas PM/MM correction : mas expression values: mas

[R] SOM object manupulation

2005-10-24 Thread Nayeem Quayum
I am trying to use SOM package to cluster some gene expression data. I got stuck with 2 questions and can't not find any documents to resolve these matters. I would really appreciate if anybody can shed some sort of light. Q1. I clustered the data using SOM function and plotted it using plot

[R] Help with SOM clustering package

2005-10-21 Thread Nayeem Quayum
Hello everybody, I am trying to use SOM package to cluster some gene expression data and there fore requesting you some help. I would really appreciate if you cold help me out. Q1. I clustered the data using SOM function and plotted it using plot function. But I can't figure out how I can list