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This simulation confirmed that again many probe sets are expected to contain one or more SNPs.
This simulation showed that many probe sets are expected to contain one or more SNPs.
In a set of biological replicates, MAS5 produced inconsistent calls for twice as many probe sets as the GM algorithm.
These annotation files report Entrez Gene ids for many probe sets, and probe sets that are annotated with the same Entrez gene id represent redundant probe sets as determined by Affymetrix.
The fold scanner script asks, for a specific combination of three comparisons (three of the letters A I), within the set of uniformly changing SSTF probe sets, how many probe sets pass the fold cutoff in all three comparisons.
The approach of Thompson et al. differed in two aspects from our study: 1) They used the Affymetrix HG-U133A GeneChip, while we used the more recent Affymetrix HG-U133 plus2.0 array, with twice as many probe sets; 2) Thompson et al. used expression values of all probe sets for clustering, while we used a set of most differentially expressed genes.
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However, even after applying these filters, many redundant probe sets showed significant fold-change differences relative to each other, suggesting differential regulation of alternative transcript production.
In resistant plants, many more probe sets detected significant changes in transcript abundance at 6 and 12 h than at 24 and 72 h.
Therefore, there can be complex, many-to-many relationships between probe sets and Gene Models.
We applied our new procedure 23 920 times to create as many random probe set pairs for human datasets.
However, the ANOVA method identified many more significant probe sets (761 versus 431).
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