[R] Calculation of normalised red and green intensities
Henrik Bengtsson
hb at maths.lth.se
Thu Jan 22 14:34:36 CET 2004
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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