Hello biostars forum,

I am new to this field of microarrays and biostatistics so my questions will surely sound clueless although I already tried to find solutions to my problem in this forum and on the internet. I hope you guys will still help me solving this.

For my studies I need to analyse two different microarray experiments, one with affymetrix data from GEO database GSE59050 and one with agilent data from GEO database GSE59408. Both are custom-commercial microarrays.

I understand that you need the corresponding CDF files for the Affymetrix microarrays to further analyse them (in this case the CDFs are called ecfs01cdf, ecfs02cdf and ecfs03cdf). Now the thing I don't really understand: do I need similar files for the Agilent microarrays? In my posted example the published data contains two files: GPL18948_platform_design_file1.txt.gz and GPL18948_platform_design_file2.txt.gz. Are this the files I need for gene annotation?

I am asking this because I got the tip to use the Bioconductor package "limma" for this single-color Agilent Experiment (like for example here) but don't know where to give in the specific platform Information.

Thank you for your help in advance, Thomas