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Removal of that sample and subsequent reprocessing of microarray data removed some of these targets from the RMA and PLIER fold change lists.
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After development of our initial network, we used microarray data to remove false-positive interactions.
I would either add all of the microarray data or remove this.
Proper normalization of microarray data can remove non-biological differences between samples due to batch effects and differences between arrays.
This step thus aims at normalizing the pre-normalized microarray data to remove artefacts and to ensure that each entry of the database follows the same procedure (see details in part 2 of the Additional File 3 and also Additional File 4).
Prior to microarray data analysis, we removed all oligonucleotide array probes that did not perfectly match both human and chimpanzee genome sequences, or had a significant difference between these two species in their hybridization patterns relative to the other probes of the same set, as described in [14].
However, in YeastNet v. 2, new filters (in particular, new probabilistic scores for protein interactions and the introduction of thresholds for DNA microarray data) down-weight or remove many false positive associations prior to integration.
To avoid this problem, microarray data were curated to remove redundant probe sets in our analysis.
Normalized microarray data were filtered to remove redundant genes and genes with minimum variation (i.e. coefficient of variation <0.3 across all samples).
Normalization of microarray data is essential for removing systematic variation and biases that are present due to the nature of the assay.
Briefly, the microarray data were filtered to remove control probe sets and those probe sets with an intensity value close to background levels.
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