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However, data missing is an inevitable phenomenon in gene expression microarray experiment due to many factors, such as instrument failure, human error.
In addition, QPCR of amplified RNA is biased towards recapitulating the results of the microarray experiment due to truncation of the RNA products.
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Real-time PCR is commonly used to validate the mRNA expressions acquired from microarray experiments due to the greater specificity of the primer vs. microarray probes[14].
Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error.
The combination of many gene expression profile datasets from different sources poses the problem of the batch effect, i.e. the systematic differences between batches (groups) of samples in microarray experiments due to purely technical reasons.
The differential regulation of TPS-a and TPS-b transcripts in grapes has not previously been reported in detail in microarray experiments due to poor coverage of the TPS gene family by the available probes.
The batch effects are the systematic differences between batches (groups) of samples in microarray experiments due to technical reasons, such as variability in materials, protocols or operators, possibly introducing a bias able to confound true biological differences (recently reviewed by Luo and coll. [ 30]).
Although more careful analysis may be advisable, it is likely this result arises from the microarray experiment itself, either due to a problem with the array hybridization or with the normalization method used at probe-sets level.
Some of the selected negative cDNA clones may have produced a weakly positive signal in northern or microarray hybridization experiments due to fairly small stretches of sequence similarity to transcripts present in glucose-grown fungus resulting in cross-hybridization.
The sample cohort differs slightly from the cohort used in the microarray experiment (see table S1) due to small amount of RNA isolated from some samples, and the inclusion of extra samples which were not used on the 96 sample microarray.
The difference in expression levels seen in between the sqRT-PCR and the microarray experiment is most likely due to cross hybridization.
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