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In the HNSCC series, there was a good correlation between several probe sets and RNU43 measured by RT PCR, but RPL3 was not associated with prognosis.
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Data were calculated from the calibration curve and normalized using the expression curve of the Actin transcript (GQ339780) corresponding to probe set Ta.28253.1.S1_at, selected among several probe sets with low variation between samples as the internal reference gene (CV = 0.036).
A scatter plot of the raw data for all transcripts of the arrays from either E-IAA negative or positive samples clearly showed several probe sets to be differentially expressed between the 2 conditions.
As shown in the top row of the Fig. 3, several probe sets show similar expression profile (slopes) between wild type and treatment (knock-out) and will be consolidated.
When several probe sets with the best extension were available, the one with the highest median value was retained.
Several probe sets may be annotated as one gene and each probe set has two repeats.
The Affymetrix Genechip HG-U133 Plus 2.0 typically contains several probe sets probing the same gene.
Transcriptome analysis revealed that several probe sets coding for MAP kinases were induced by SnTox3.
Several probe sets involved in proline accumulation were also classified in these clusters (detailed hereafter).
In case several probe sets share the same gene symbol, the probe set with the largest mean expression over all samples was used as representative for that symbol.
Several probe set algorithms were available for processing microarray data.
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