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The assumption of normality is rarely satisfied in microarray data even after normalization.
Another example is a single-gene network inferred from microarray data even though the samples may be collected over a time course or multiple conditions.
No resource can currently identify expression pattern of specific mRNA forms using these microarray data, even though it is possible to do this.
For rectal carcinomas, the observed high variation in percentages of epithelial tumor surface might complicate interpretations of microarray data even more.
In contrast, the expression patterns of the other genes were very similar to microarray data, even though observed differences were not always significant.
However, we did not observe significant 3' bias as we were able to correlate our microarray data even though the qRT-PCR primers were selected from sequences away from the 3' end of the transcripts.
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The microarray data revealed, even under stringent criteria (False Discovery Rate at q < 0.005), a large number of differentially-expressed genes (1235 to 1978) upon HacA activation (Table 1).
This indicates the need of robust noise models, which can handle outlying data points well and suggests that Gaussian noise models are unsuitable for microarray data analysis, even if according to Novak et al. (2006) only about 5 15% of samples are non-Gaussian distributed.
For those 24 genes, the expression ratios calculated from QPCR and microarray data are consistent even if some limited differences exist, mostly due to the underestimation of highest differential expression by nylon array technology (Table 2).
Quantitative-PCR (qPCR) analysis of miR-155 expression confirmed our microarray data (Fig. 1B), even when a lower multiplicity of infection (MOI) was used (MOI 10 and 50; data not shown).
As industry and regulators wrestle with the intricacies of microarray data formats and submission, even more complex challenges loom: the data produced by proteomics and metabolomics research.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com