Plants are sessile organism and their ability to adapt stress is crucial for survival in natural environments. They do respond to high temperatures by synthesizing a group of proteins called Heat Shock Proteins. Heat shock proteins (HSP) are expressed in response to various biological stresses, including heat, high pressures, and toxic compounds. It is also one of the most abundant cellular proteins found under non-stress conditions. Although the gene expression patterns from different accession tend to be similar but it differ towards development stage. The aim of this study is to conduct quality assessment of Arabidopsis Thaliana microarray data and also to determine deferential gene expression using R programming environment. RMA procedure was used for background correction, normalization of the probe-level data to obtain differentially expressed genes and their expression. MA plots presented expression level of data. Online tool GENEVESTIGATOR was used to analyze Arabidopsis differentially expressed genes obtained from Bioconductor. This program is publically available database having several genes with known expression patterns. This study revealed the similarities among differentially expressed genes obtained from Bioconductor and online analysis tools GENEVESTIGATOR. Certain likely factors causing discrepancies in the gene expression are also reported in this study.