[BioC] Agilent two color Quantile normalization

[James W. MacDonald]

Hi Neeraj,

>From ?normalizeBetweenArrays:

object: a numeric ‘matrix’, ‘EListRaw’, ‘RGList’ or ‘MAList’ object
          containing un-normalized expression data.  ‘matrix’ or
          ‘EListRaw’ objects will be assumed to contain single-channel
          data, usually log-intensities, whereas ‘RGList’ or ‘MAList’
          objects should contain two-color data.


On Wednesday, September 11, 2013 10:08:38 AM, Neeraj Rana wrote:
> Dear Bioconductor List,
>
> I am doing two color Agilent microarray analysis by limma.
>
> I tried to normalize* M *values by using following command.But both the
> commands are giving different M values.
>
> *(1) MA<- normalizeBetweenArrays (MAw, method="quantile")

So here limma thinks you have a two-color array.

>
> *
> *(2) MA <- **normalizeBetweenArrays (MAw$M, method="quantile")

And here limma thinks you have a one-color array. Since you do not have 
a one-color array, this is not what you should be doing.

Best,

Jim




>
> *
> the first command does not give same boxplot of M value for all arrays ,
> but second command is giving same boxplot for all arrays.*
>
> *
> *I want to know whether first command is proper for between the array
> normalization and is it applied on M values or not?
>
> *
> Thanks *
> *
> *
> **
> *
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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