Array express microarray single channel agilent data only contain Green.DerivedSignal values??

Question

[firstorthopedicdoctor]

Dear colleagues I am doing microarray meta-analysis and I am using the E-MTAB-2325 data from the array express database. It is a single channel Agilent Whole Human Genome Microarray 4x44K 014850 G4112F. I downloaded the rawdata which is only one text file conaining Green.DerivedSignal values. How should I start the processing of this data? should I start with log2 then normalization. I have searched papers that used this data and some papers did background correction, is this possible with these data?

head(raw_data)
1 09-13-07.gpr          12bis 09-13-07.gpr                     14 09-13-07.gpr 
228.00000                  850.00024                                191.99998       
30.99999                    45.00000                                 11.00000   
1184.00010              1574.99950                               461.00012      
1211.99960              3452.99950                            1256.99990    
199.99998                  934.00020                                 152.00002      
36.00000                99.99999                                    30.00001    

Answer 1

[Kevin Blighe]

We may normally read these files via limma, as follows:

data <- read.maimages(files = files, columns = 'Green.DerivedSignal')

where files is a character vector of individual sample files, and data would then be an EListRaw object, requiring further normalisation.

In this case, the authors seem to have placed all sample data into the same file, which is quite frustrating. You may have to 'hack' an EListRaw object and then attempt to normalise it by following my code here: How to process (seems) Agilent microarrry data?

Otherwise, just contact the authors and request the original raw gpr files, and / or the normalised expression matrix.

Kevin