I have about 600 genes of a superfamily, Now I tried to analyze their expression pattern through bioinformation method, many papers told me that Microarray data can be used to find genes expression characteristics in different tissues but the methods which they described were not clear and I don't know how to do it.
I pasted the correspondent method of one paper here:
Microarray-based expression analysis of ZmPK genes
To analyze the expression pattern of the ZmPK genefamily among different organs and development stages,transcriptome data of the genome-wide gene expressionatlas of maize inbred line B73 were obtained from the publicly available database PLEXdb with the accessionnumber ZM37 (BarleyBase/PLEXdb). This microarraywas made by NimbleGen, containing 80,301 probe setsto profile transcription patterns in 60 distinct tissuesrepresenting 11 major organ systems of inbred line B73.The maize tissues/organs and developmental stagesselected for microarray analysis include germinatingseed, root, whole seedling, stem and shoot apicalmeristem, internodes, cob, tassel and anthers, silk, leaf,husk and seed. The data were normalized using a robustmulti-chip average (RMA) algorithm. Log2-trans-formed expression values were loaded into R (v15.2)and Bioconductor for expression analysis (http://www.bioconductor.org/). Limma, a software used to analyze gene expression data, was used for data processing, and heat maps representing log2-transformed probe intensities were generated with the gplots package.
If you some suggestion, please tell me .
I am a newer of bioinformatics, I don't need detail pathway, I just need crude flows such as what packages and parameters used.