[BioC] normalization for data in a matrix

[Federico Abascal]

Hello,

I have been reading about methods of normalization for microarrays
intensities and found diverse bionconductor packages (affy, limma,
aroma) implementing different approaches. I am still lost with so many
information. To test the different methods I would like to use my own
matrix of intensities (I have no other information than intensities). My
question is, which is the best (or easiest) way to test the different
normalization methods with a matrix as the one I have?

In addition, I would like to know if normalizing by dividing the
intensity of each gene by the sum of intensities in the corresponding
array ("Total Intensity Normalization") is a bad approach?

I found that genes around particular rows (e.g row 2000, row 10000, etc)
tend to have greater intensities accross all of the samples (the array
is Affymetrix GeneChip Human Genome U133 Plus 2.0 Array). An example of
this for a particular hybridization can be found at:
http://biocomp.cnb.uam.es/~fabascal/tmp.png
At least most of these peaks are related to ribosomal proteins, what
explains the increased expression. What I do not understand is why those
increased measures tend to appear together, in blocks. Could be this an
artifact? Does it require a correction? How could it be corrected? These
might be too many questions, sorry!

Thank you!
Federico