[BioC] abnormal distribution after GCRMA

[Zhijin Wu]

Hi, Philippe, 
 Please check my reply to you earlier today
Jean

On Thu, 19 Aug 2004 Phguardiol at aol.com wrote:

> Hi,
> I have data obtained with the following procedure under R2.0dev / XPPro / PC32bits: triplicates of 4 different conditions under Affy MmU74Av2. cells obtained from mouse.
> 
> data <- ReadAffy()
> data2 <- gcrma(data)
> 
> I used the development version of GCRMA1.1.0 and AFFY downloaded/updated today.
> 
> and If I look at the distribution of the intensities after gcrma I obtain an usual plot (see attached). I have attached the degradation plot that for me seems to be fine but the ends (any comments on these ?), and the histogram obtained after hist(data) which identify 3 chips with different profiles. 
> I have never worked with gcrma and mouse chips but I m very surprised of the 2-peak plot after GCRMA; is it a problem of saturation ? or can we suspect that all these 12 samples that look all the same had 2 cell populations inside ??? I doubt about that... any other option ? a problem in GCRMA ? second question, shall I avoid using the 3 chips with very different profiles after hist(data) ? they seem to be fine after GCRMA.
> thanks for your help
> Philippe
>