normalization with Expression Set file

Question

[vahideh]

hello how I can normalize ExpressionSet file?( I downloaded a GSE, and it does not have a Supplementary File). I try to normalize this file with normalize.ExpressionSet.quantiles() function in the affyPLM package, but its QC boxplot (and other diagrams) does not change before and after normalization.

is there another packages or functions to this purpose?

can I normalize samples with the following data with the limma package?

Thank you.

> !Sample_series_id = GSE3591                                           
>  !Sample_data_row_count =14400                                            
> #ID_REF =                                             
> #CH1_MEAN = Cy5 Mean Foreground                                           
> #CH1_SD = Cy5 Foreground SD                                           
> #CH1_BKD_MEAN = Cy5 Mean Background                                           
> #CH1_BKD_SD = Cy5 Background SD                                           
> #CH2_MEAN = Cy3 Mean Foreground                                           
> #CH2_SD = Cy3 Foreground SD                                           
> #CH2_BKD_MEAN = Cy3 Mean Background                                           
> #CH2_BKD_SD = Cy3 Background SD                                           
> #VALUE = Log ratio (log2 of PRE_VALUE)                                            
> #PRE_VALUE = (Cy5 Foreground – Background) / (Cy3 Foreground – Background)                        
> !sample_table_begin                                           
> ID_REF    CH1_MEAN    CH1_SD  CH1_BKD_MEAN    CH1_BKD_SD  CH2_MEAN    CH2_SD  CH2_BKD_MEAN    CH2_BKD_SD  VALUE   PRE_VALUE   
> 1 42  16  30  8   88  76  64  15  -1.19   0.48    
> 2 41  14  30  7   83  24  60  14  -0.85   0.55    
> 3 31  11  30  7   65  15  61  31  null    0.33    
> 4 45  12  30  7   90  24  60  12  -0.61   0.5  5  33  10  30  7   68  17  59  13  null    0.3

Answer 1

[mastal511]

The affy package can do normalisation, but if your boxplots don't change before and after, it may be that the data has already been normalised.

[vahideh]

thank you for your response. I sure that my data is raw, it has been mentioned in the GSE's metadata. And that this array is Spotted Oligonucleotide not Affy, I don't know that the affy package can normalize it or not!