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The unexpected outlier position of GBS gene transcript data from donor A blood was confirmed by a second set of microarray data (data not shown).
The acoB gene (GBAA2775) was used as the internal reference, as it was observed to have no change in expression on microarray data (data not shown).
A majority of the comparisons (8/11 genes) via qRT-PCR were in agreement with the microarray data (data not shown).
We also confirmed this expression pattern on independent microarray data (data not shown but can be accessed on our microarray expression atlas Amazonia! (http://amazonia.transcriptome.eu/)).eu/
Although these genes did not meet significance criteria on qRT-PCR, there is a strong correlation between the qRT-PCR data and the microarray data (data not shown).
All of the removed transcripts were confirmed as low expressed transcripts in the MUTZ-3 cell line based on microarray data (data not shown).
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To combine microarray and qPCR data, data were median-centered as described previously [ 3].
The results were in agreement with the cDNA microarray and 2D gel data (data not shown).
The mRNA microarray data obtained our previous microarray data of CAFs and NFs.
We discuss statistical issues arising in analyzing population genetics data, gene expression microarray data, next-generation sequencing data, microbiome data, and network data.
Image analysis is an important part of the process of generating good quality microarray data, prior to data mining.
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