abnormal distribution after GCRMA
1
0
Entering edit mode
@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
gcrma gcrma • 951 views
ADD COMMENT
0
Entering edit mode
Zhijin Wu ▴ 410
@zhijin-wu-438
Last seen 10.2 years ago
Hi, Philippe, Please check my reply to you earlier today Jean On Thu, 19 Aug 2004 Phguardiol@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 >
ADD COMMENT

Login before adding your answer.

Traffic: 807 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6