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These studies are somewhat limited because they either use small microarrays, examine animals shortly after colitis induction (consistent with acute but not chronic colitis), offer limited or no postgenomic validation or use longitudinal tissue samples.
In general, these studies have addressed acute colitis (48 72 h after induction), employed small microarrays (containing 87 and 1252 transcripts in two of the studies), have analysed large samples (augmenting internal genomic variation, which occurs along the longitudinal axis) and include modest validation experiments (6 14 genes).
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The previous EST sequencing efforts for the B biotype whitefly have allowed the development of small-scale microarrays for gene expression analysis in the context of insecticide resistance and parasitoid-whitefly interactions [ 13- 15].
These EST datasets have been used to develop small-scale microarrays for gene expression analysis in several coral-algal symbioses: Acropora millepora, Acropora palmata and Montastrea faveolata [ 25- 27].
These EST sequencing efforts have allowed development of small-scale microarrays for gene expression analysis in the context of coral stress physiology [ 14], and similar studies aiming to identify stress candidates are currently underway [ 13].
It is evident that prior biological knowledge is not always available and thus no requirements with respect to the expression levels and/or differentially expressed genes can be formulated, e.g. if so far unknown biological phenomena are studied with small-scale microarrays.
The method was tested on several relatively small microarray data sets (n = 53 to 280).
Thus, the variance stabilized t-type score is effective and robust for identifying differentially expressed genes in small microarray experiments.
To allow detailed expression analyses of the various E. histolytica peptidase genes, a small microarray was designed.
It should be acknowledged that very small microarray studies may have too few samples to support permutation.
Yang and Churchill have noticed the problem of permutation-based methods when applied to small microarray experiments [ 8].
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