[BioC] Strange signal Log-Ratios with MA.RG

[Sean Davis]

On Apr 1, 2005, at 11:06 AM, Giulio Di Giovanni wrote:

> Hi to all,
>
> I have a problem that really I cannot solve.
>
> Some signal log-ratios given to me converting a RGlist with MA.RG(RG) 
> are different from the ones calculated directly, that's the point:
>
> Looking some .gpr files, I build a RGList with
>
> RG <- read.maimages(source="genepix", ext="gpr)
>
> and I obtain for the first 3 genes and the first sample the following 
> Red and Green Foreground and Background intensities
>
> RG[1:3,1]
> An object of class "RGList"
> $R
>     63MG
> [1,]  407
> [2,] 4304
> [3,]  531
>
> $G
>     63MG
> [1,]  291
> [2,] 3571
> [3,]  394
>
> $Rb
>     63MG
> [1,]  518
> [2,]  518
> [3,]  493
>
> $Gb
>     63MG
> [1,]  295
> [2,]  295
> [3,]  302
>
> That's to say that log ratios are:
>
>> za <- log2((RG$R[1:3]-RG$Rb[1:3])/(RG$G[1:3]-RG$Gb[1:3]))
>> za

Note here that RG$R[1:3] is not necessarily the same as RG$R[1:3,1].  
Same goes for other RG stuff in your example.

> [1]  4.7944159  0.2087391 -1.2756344
>
> But when I made the conversion with MA.RG(RG) (I need that for 
> following analysis)
> I obtain:
>
>> RGMA <- MA.RG(RG)
>> RGMA$M[1:3,1]
> [1]         NA  0.2087391 -1.2756344
>
> And this happens for several other genes and samples. Most values are 
> exactly equal, others have NAs ...
>

Note that for the first gene, you will have a negative values in red 
and green channels.  If you type MA.RG in your window, you will see 
that it sets RG$R values <=0 after background substraction to NA; same 
for RG$G.  I think MA.RG is probably doing the right thing here. Do you 
agree?

Sean