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Data presented here document reductions in Cy5 signal on both in-house produced microarrays and commercial microarrays as a result of exposure to unfiltered air.
In one direction, for the list of DEGs detected in the oligo microarray data, we measure its reproducibility in the cDNA microarray data as the percentage of these DEGs, which also appear in the cDNA result.
In another direction, for the DEG list detected in the cDNA data, we measure its reproducibility in the oligo microarray data as the percentage of the detected DEGs, which also appear in the oligo microarray result.
Although QPCR results showed higher fold changes than the microarray data, they supported the microarray data as to direction of change for the majority of the genes tested.
Critical to the sharing of microarray data is providing raw microarray data as opposed to processed data.
As a result of the high defensin levels identified in the microarray data, defensin-α1 was chosen for further analysis.
Therefore, we analysed the changes occurring as a result of miR-145 overexpression in PC3 cells using mRNA microarray (data not shown).
Several recent articles have provided substantial evidence that systematic noise introduced as a result of batch-processing have a detrimental effect on data derived from microarrays [ 1- 5].
Genes with altered gene expression as a result of the downshift have been catalogued based on Rank product analysis of the microarray data (Additional file 5).
A subset of genes was validated by qRT-PCR and results were correlated well with microarray data indicating that microarray results provided an accurate report of transcript level.
As a result, the interpretation of DNA microarray data obtained under a large number of conditions has become a challenging problem.
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