[BioC] Error normalizing merged data sets

[Mark Cowley]

Hi Amit,
from your error:
> Error in log(R, 2) : Non-numeric argument to
> mathematical function.


this means that the code is trying to log transform non-numerical  
data, which usually means at least one of your numbers is actually a  
character, thus the whole column becomes characters.
I'd check your "R" object thoroughly for the presence of "character"  
data

Mark
On 30/09/2009, at 6:33 AM, Amit Kumar wrote:

> Dear All,
>
> I am working with 13 different data sets (containing 550 arrays in
> total) which is normalized using general linear model for print-tip. I
> am trying to do following:
>
> 1) Merging all 13 different data sets:
> To merge these data sets I built ExpressionSet for each data set. Then
> I made a list of these ExpressionSets and named it "fullset1". Then to
> merge red and green intensity I did following:
>
> red1 = lapply(fullset1,function(eset) exprs(eset)[2:23689,seq(1,
> ncol(eset), 4)]) # These columns contain normalized Red intensity in
> each data file.
> red = do.call(cbind, red1)
>
> green1 = lapply(fullset1,function(eset) exprs(eset)[2:23689,seq(2,
> ncol(eset), 4)]) # These columns contain normalized Green intensity in
> each data file.
> green = do.call(cbind, green1)
>
> 2) Normalizing between arrays:
> I am using normalizeBetweenArrays (method=quantile) for merged data
> set so that the intensities have similar distributions across the
> series of arrays. So I did following:
>
> rgl1 = new("RGList", list(R=red, G=green))
> norm1 = normalizeBetweenArrays(rgl1, method="quantile")
>
> And got error: Error in log(R, 2) : Non-numeric argument to
> mathematical function. Why this error??
>
> Then I tried to normalize red and green intensities separately by  
> doing this
> normR1 = normalizeBetweenArrays(red, method="quantile")
> normG1 = normalizeBetweenArrays(green, method="quantile")
> and it worked! Why??
>
> 3) Quality assessment of the merged data set:
> For quality assessment I am using arrayQualityMetrics package. To
> check if quality assessment on separately normalized red and green
> intensities can be performed I did following:
> rgl1 = new("RGList", list(R=normRed1, G=normGreen1))
> qmrgl1 = arrayQualityMetrics(rgl1, "QMrgl1") # Here the package is
> accepting expression data as RGList (rgl1) and will generate HTML
> report and save in QMrgl1 folder.
>
> But with no luck I got error: Error in rc - gc : non-numeric argument
> to binary operator
>
> I am really stuck and running out of idea. Please help me to rectify
> these errors. Thanks in advance.
>
> Best!
> Amit
>
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