thanks jim

But when i use normalizeBetweenArrays(MA,methode="quamtile),it is supposed
to perform quantile normalization on M values and the mean ,median,maximum
value and minimum value should be the same of all arrays after
normalization.
I am copying my script here for reference.
> targets <- readTargets("target.txt")
> targets
           FileName    Cy3    Cy5
1   207_1_1_4HR.txt  4HCY3  4HCY5
2   207_1_2_4HR.txt  4HCY3  4HCY5
3   207_1_3_1HR.txt  1HCY3  1HCY5
4   207_1_4_1HR.txt  1HCY3  1HCY5
5 8052_1_3_12HR.txt 12HCY3 12HCY5
6 8052_1_4_12HR.txt 12HCY3 12HCY5
> RG <- read.maimages(targets, source="agilent")
Read 207_1_1_4HR.txt
Read 207_1_2_4HR.txt
Read 207_1_3_1HR.txt
Read 207_1_4_1HR.txt
Read 8052_1_3_12HR.txt
Read 8052_1_4_12HR.txt
> MA <- normalizeWithinArrays(RG,method="loess",bc.method="normexp")
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 4 corrected
Array 5 corrected
Array 6 corrected
> *summary(MA$M)*
  207_1_1_4HR         207_1_2_4HR         207_1_3_1HR
207_1_4_1HR        8052_1_3_12HR       8052_1_4_12HR
 Min.   :-8.853926   Min.   :-9.948604   Min.   :-6.767666   Min.
:-6.642965   Min.   :-5.344051   Min.   :-6.576922
 1st Qu.:-0.395661   1st Qu.:-0.024118   1st Qu.:-0.364050   1st
Qu.:-0.339771   1st Qu.:-0.308643   1st Qu.:-0.352430
 Median :-0.002921   Median :-0.005917   Median :-0.007129   Median :
0.003566   Median : 0.007702   Median : 0.007684
 Mean   : 0.013726   Mean   : 0.002334   Mean   : 0.043019   Mean   :
0.002412   Mean   :-0.001696   Mean   :-0.012679
 3rd Qu.: 0.412789   3rd Qu.: 0.013281   3rd Qu.: 0.412566   3rd Qu.:
0.342954   3rd Qu.: 0.311236   3rd Qu.: 0.349261
 Max.   : 4.826212   Max.   : 3.977841   Max.   : 4.061991   Max.   :
4.568052   Max.   : 4.140642   Max.   : 4.218073
> *MA <- normalizeBetweenArrays(MA,method="quantile")*
>* summary(MA$M)*
  207_1_1_4HR         207_1_2_4HR          207_1_3_1HR
207_1_4_1HR        8052_1_3_12HR       8052_1_4_12HR
 Min.   :-6.921310   Min.   :-13.368132   Min.   :-5.118688   Min.
:-6.108837   Min.   :-4.488686   Min.   :-5.388395
 1st Qu.:-0.344347   1st Qu.: -0.238684   1st Qu.:-0.328855   1st
Qu.:-0.316487   1st Qu.:-0.281210   1st Qu.:-0.344085
 Median :-0.029286   Median :  0.009940   Median :-0.047600   Median :
0.000221   Median :-0.000253   Median :-0.002598
 Mean   :-0.000028   Mean   :  0.000014   Mean   :-0.000024   Mean
:-0.000030   Mean   : 0.000019   Mean   : 0.000045
 3rd Qu.: 0.312078   3rd Qu.:  0.244628   3rd Qu.: 0.287170   3rd Qu.:
0.315771   3rd Qu.: 0.273066   3rd Qu.: 0.341673
 Max.   : 5.689074   Max.   :  5.190544   Max.   : 5.034104   Max.   :
5.185184   Max.   : 4.800180   Max.   : 5.212559

thanks


On Wed, Sep 11, 2013 at 8:04 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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 *
>> *
>> *
>> **
>> *
>>
>> --
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>



-- 
Neeraj KumarMolecular Reproduction Development and Genetics
Prof. Kondaiah' Lab
Indian Institute of Science
Bangalore 560012
Mobile # +91-9986295625

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