Calculation of normalised red and green intensities
Hi, here's the calculations M = log2(R/G) = [log rules] = log2(R)-log2(G) (1) A = 1/2*log2(R*G) = [log rules] = (log2(R)+log2(G))/2 (2) where log2(x) is the logarithm of x with base 2. If R,G > 0, there is a one-to-one relationship between (A,M) and (G,R) as follows R = (2^(2A+M))^(1/2) = sqrt(2^(2A+M)) (3) G = (2^(2A-M))^(1/2) = sqrt(2^(2A-M)) (4) It's a good exercise to verify the correctness, by replacing R and G in (1) and (2) with the expressions for R and G in (3) and (4). I believe there are methods in the marray packages for calculating R and G from M and A like the above, but I don't know the exact name of them. BTW: I think it's better to ask these type of questions to the Bioconductor (of which marrayNorm is part of) mailing list instead. Best wishes Henrik Bengtsson Lund University, Sweden
-----Original Message----- From: r-help-bounces at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Binita Dutta Sent: den 22 januari 2004 13:47 To: R-help at stat.math.ethz.ch Subject: [R] Calculation of normalised red and green intensities Dear Sir/Madam, I could succesfully normalise my microarray data using marrayNorm package. However, i have not been able to get normalised red and green
channel
intensities through R package. Is there a possibility to write a formula to calculate back the red and green channel intensities after normalisation of the data. Do I need to incorporate this formula in my R script? I am biologist ans would seek your help to write this formula. Thanking you, Binita Dr. Binita Dutta MicroArray Facility(MAF) UZ Gasthuisberg Onderwijs en Navorsing Herestraat 49 3000 Leuven Belgium
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