R help - Mar 2004 - X11 and utils

Hello,
I'm a french student working on a project concerning cDNA microarray.
I've chosen to work with R and use the marrayClasses, marrayInput (...)
packages.

First, when I enter "library(marrayInput)", R warns me about a missing
package called "utils" but I can't find it anywhere. Normally this
package
is installed when you install "base" package. Moreover when I call a
function of the "utils" package, it works so it seems to be installed.
Why doesn't R see it when I enter "library(marrayInput)" ?
I hope, I am clear enough.

Secondly, once R is installed, X11() does not work. I can't see anything
when I invoke the plot functions.
Maybe I have to precise that :
      - I work on a Linux platform. But I havn't got the root's
password.
      - So I can only install R locally
My first idea is that the problem comes from the intallation step. Is
there something to tell R about the system X11R6 path ? May I give a
parameter to ./configure ? Or does R normally find all of these itself ?


waiting for an answer,
thank you very much

kind regards,
Anthony Ferrari
anthony.ferrari at ensimag.imag.fr

Hello,
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 !!

thanks

Best regards,
Anthony Ferrari