AM collected the data, carried out the initial microarray analyses and interpreted the data.
As a result, it was suggested that data from microarray analyses be interpreted with caution.
BG was involved in the experimental design and in planning the study, carried out sample collection, extracted RNA, carried out microarray molecular work, RT-PCR and real-time PCR work, performed statistical analyses, interpreted data and drafted the paper.
Any study using a similar amplification protocol coupled to LCM-based microarray analyses may find this data useful in interpreting the results.
As such...., microarray analyses comparing these "tumor" with "normal" samples are difficult to interpret, since gene expression in tumor epithelial cells was diluted by the inclusion of adjacent stromal cells in the analysis, leading to ambiguous results.
Comparing microarray analyses between different platforms and labs is a difficult task and the results have to be interpreted cautiously.
Importantly, when synthesizing results across studies, our findings must be interpreted with caution due to different time points and species of infection used in these three microarray analyses.
Previously, we illustrated the impact of SNPs on gene expression microarray analyses [ 14] and argued that complete SNP masks for gene expression microarray and other hybridization techniques are essential to appropriately interpret these data.
However the advantages of microarray analyses, using changing patterns of transcription (through identification of co-regulated genes and the modified expression of defined functional categories) to interpret biologically significant scenarios, are still applicable using amplified RNA.
Work flow for microarray analyses.
