R help - Jan 2004 - 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

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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