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The genes identified by microarray analyses were challenged for gene function.
The differences in gene expression found by microarray analyses were validated by real-time PCR.
The genes identified by microarray analyses were selectively validated by real-time RT-PCR of the same pooled RNA as used for chip analyses.
As summarized in Table 2 (Additional File 3), the values for induction and repression of transcription obtained by microarray analyses were clearly confirmed by quantitative PCR.
The expression patterns observed by microarray analyses were consistently confirmed by RT-qPCR for genes associated to cell wall metabolism, redox system and photosynthesis (Additional file 2: Figure S1).
The gene expression values obtained by microarray analyses were concordant with EGFR detection on the protein level measured by IHC with p < 0.01 for probe set 201983_s_at, and p < 0.02 for probe set 201984_s_at (Spearmans Rank Order Correlation, see fig. 2 and 3).
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The enormous amount of data generated by microarray analyses is a challenge even in small studies, easily summing up to several gigabyte of raw expression data.
Depending on the probe sets analyzed, the correlations between qRT-PCR data and microarray signal intensity varied from 0.531* to 0.932**, indicating that the expression patterns detected by microarray analyses are in good agreement with that detected by qRT-PCR.
The Msl1-, or Nsl1-KD affected genes determined by the microarray analyses were then confirmed by RT-qPCR under Msl1-, or Nsl1-KD conditions.
Subsequently, microarray analyses were validated by RT-PCR and qRT-PCR.
Microarray analyses were performed by YXY and PP.
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