[R] marrayNorm package

anthony.ferrari@ensimag.imag.fr ferraria at ensisun.imag.fr
Fri Apr 2 11:48:58 CEST 2004

I'm a french student working on cDNA microarrays.
I decided to use the bioconductor packages and I have a problem with
normalization functions.

As everybody who manipulates microarray data know, there are some spots
on the slide which are to be removed. In the marrayLayout there is a slot
"maSub" (logical vector) where one can define the good spots.
Besides, when you print the features of your slide there is a line :

"Currently working with a subset of 18482 spots"

so it seems to be good.
BUT the problem is that the functions of marrayNorm package don't seem to
take the subset into account even when you fill the field 'subset' with
the 'maSub' vector.

It seems to be the same with for instance the 'maPlot' function. It plots
all the spots of the array without taking the 'maSub' vector into account.

Anyone who can help me ?
I need help !!


Best regards,
Anthony Ferrari

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