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Phguardiol@aol.com
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@phguardiolaolcom-152
Last seen 10.2 years ago
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