The same RNA samples had been analyzed by two different platforms: DGE and RT-PCR - Life Technologies.
However, because overall shifts in signal intensities as measured by two different platforms can easily have a technical origin we have sought to independently verify the effect using quantitative real-time PCR (QPCR).
Since gene expression profiles of two data sets are conducted by two different platforms and thus have significantly different magnitudes (Fig. 4a), we first removed the batch effects using the ComBat function in R (Fig. 4b).
The combined data set had 12 post-ischemia time-points represented by five different platforms (ABI, Affymetrix, Agilent, Amersham, and Illumina) and four species (human, pig, rat, and mouse) and was stratified by the recovery time after ischemia (Table 1).
Each of the methods uses different pipelines offered by four different platforms, including Genome Trax of BIOBASE (Qiagen, Beverly, MA, USA), Ingenuity Variant Analysis (Qiagen, Redwood City, CA, USA), Diploid genome interpretation service (Diploid Genomics, Leuven, Belgium), and GeneTalk (Gene Talk Berlin, Germany).
A comparison of miR-34 family miRNA expression measured by the two different platforms is shown in Figure 3.
Detection of SNVs and small InDels by these two different platforms demonstrated its complementary power; whereas Illumina GA provides a significant depth (67× in this case) useful for resolving many SNVs and small InDels, the length of 454 reads allows for the detection of these GVs in highly polymorphic regions.
We further examined the reproducibility of miRNA expression experiments across two different platforms by comparing RT-PCR and microarray results.
Here we have used the Rank product [ 19] method to detect differentially expressed genes in response to E2 treatment in MCF-7 cell lines, by integrating multiple array datasets from two different platforms across laboratories.
Although MPSS and SBS are two different platforms, the transcriptomes generated by the two methods were highly correlated in our study.
That was indirectly proven by SWP validator which performs same diagnostic software on two different platforms.
