Hi, I am trying to process microarray data from Array Express through ArrayExpress package for R. This is an old non-affimetrix microarray of two colours with the accession code "E-MEXP-42". It has multiple array designs, so when I process it with the ArrayExpress package it creates a NchannelSet for each one, four in total. Apparently, a list of objects is generated but I can't access to each array data set and I don't know how process this data. If I ask for the class of the elements of the list I get "list" class, no nchannelset class how I expect. Could anyone help me to process this data? I only need a table with the mean and background intensity of each spot and the genes associated. Here is my code:

AEset = ArrayExpress("E-MEXP-42", dataCols = list(R = "Software Unknown:SR_Mean", G = "Software Unknown:SG_Mean", Rb = "Software Unknown:SR_bkMean", Gb = "Software Unknown:SG_bkMean"))

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-MEXP-12/A-MEXP-12.adf.txt' Content type 'text/plain' length 907006 bytes (885 KB) downloaded 885 KB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-MEXP-23/A-MEXP-23.adf.txt' Content type 'text/plain' length 938590 bytes (916 KB) downloaded 916 KB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-MEXP-24/A-MEXP-24.adf.txt' Content type 'text/plain' length 926200 bytes (904 KB) downloaded 904 KB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-MEXP-25/A-MEXP-25.adf.txt' Content type 'text/plain' length 939358 bytes (917 KB) downloaded 917 KB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-42/E-MEXP-42.sdrf.txt' Content type 'text/plain' length 30338 bytes (29 KB) downloaded 29 KB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-42/E-MEXP-42.idf.txt' Content type 'text/plain' length 15101 bytes (14 KB) downloaded 14 KB

Copying raw data files

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-42/E-MEXP-42.raw.1.zip' Content type 'application/zip' length 56417323 bytes (53.8 MB) downloaded 53.8 MB

Unpacking data files ArrayExpress: Reading pheno data from SDRF ArrayExpress: Experiment uses multiple Array Designs. A separate expressionSet will be created for each ArrayExpress: Reading data files Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198796961.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198796931.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797486.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797021.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797516.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198796991.txt ArrayExpress: Reading feature metadata from ADF Read 48 items ArrayExpress: Reading data files Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797201.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797546.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797441.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797081.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797291.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797576.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797171.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797471.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797051.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797321.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797141.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797351.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797231.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797411.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797111.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797381.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797261.txt ArrayExpress: Reading feature metadata from ADF Read 48 items ArrayExpress: Reading data files Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797066.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797306.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797216.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797561.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797426.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797036.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797336.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797186.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797456.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797126.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797366.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797246.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797156.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797096.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797276.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797531.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797396.txt ArrayExpress: Reading feature metadata from ADF Read 48 items ArrayExpress: Reading data files Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198796946.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198796916.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797006.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198797501.txt Read C:\Users\yamil\AppData\Local\Temp\RtmpUdaoHj/E-MEXP-42-raw-data-198796976.txt ArrayExpress: Reading feature metadata from ADF Read 48 items

E-MEXP-42 was successfully loaded into 4 NChannelSet

E-MEXP-42 was successfully loaded into 4 NChannelSet

E-MEXP-42 was successfully loaded into 4 NChannelSet

E-MEXP-42 was successfully loaded into 4 NChannelSet

class(AEset) [1] "list"

class(AEset[1]) [1] "list"

Regards,