Because there is a possibility that genes with high expression show weak response to perturbations simply due to saturation or miscalibration of microarray signals, we tested the sensitivity of the microarray by serial dilution of mRNA [ 14].
Microarrays, on the other hand, are known to suffer from reduced dynamic range of signals due to saturation biases and high background, and non-specific or cross-hybridization resulting in false-positive signals, especially for transcripts that have low expression levels.
The microarray signals were analyzed using the Affymetrix RMA algorithm.
Microarray signals were determined using Affymetrix Microarray Suite 5.1.
To compare qPCR-array and microarray assays, the log2 of microarray signals was used.
At higher BMD(L) estimates RNA-Seq values were higher, likely due to microarray signal compression.
cbh1 and egl1 genes were detected to have a higher expression level in D03 cultivations than in D06 cultivations by microarray, TRAC and previously by Northern [ 32], but their differential expression was not statistically significant with the cut-offs used, possibly due to microarray signal saturation.
The lower microarray signal in the fha-repeat can be due to a complete loss of these genes, a lower copy number or a high sequence divergence compared to the reference strain.
cel7a/cbh1, the major cellobiohydrolase, is co-regulated with cel6a/cbh2, but due to saturation of the microarray signal for this transcript, we were not able to use the transcript pattern of cel7a/cbh1 to evaluate coregulated genes of cellulases.
Moreover, such copy numbers or genotypes are often incorrectly determined when microarray signal intensities derived from different copy numbers or genotypes are not clearly separated due to noise.
