search for: arrayquality

Hi, folks: I have used R for some time and have not explore deep inside the codes of the packages. Today, I try to modify some code in a package of arrayQuality (I do not think it matters which package it is). There is a function called maQualityPlots and I use fix(maQualityPlots) that I can view and edit the code of this function. However, there is another function qpMAPlots that I want to edit, 1. I type in ?qpMAPlots, it says: Internal functions...

Does anyone have nice quality controlls for affy arrays,.... Can't find any tools as are being used for 2 dye arrays..... cheers, marinus This e-mail and its contents are subject to the DISCLAIMER at http://www.tno.nl/disclaimer/email.html [[alternative HTML version deleted]]

...ffypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQuality, LPE) -- sequence analysis (pairseqsim, Biostrings) -- interface to the GeneSpring data analysis program (GeneSpring) TOOLS: ====== The released packages include tools which facilitate: * annotation * data management and organization through the use of the S4 class structure * identific...