[BioC] Re: [R] marrayNorm package (fwd)

[anthony.ferrari at ensimag.imag.fr]

---------- Forwarded message ----------
Date: Fri, 2 Apr 2004 08:38:45 -0800 (PST)
From: Douglas Grove <dgrove at fhcrc.org>
To: "anthony.ferrari at ensimag.imag.fr" <ferraria at ensisun.imag.fr>
Subject: Re: [R] marrayNorm package

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On Fri, 2 Apr 2004, anthony.ferrari at ensimag.imag.fr wrote:

>
> 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
>
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