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We use the same normalization method as in [ 19], which includes base 10 log-transformation as well as normalization to mean 0 and variance 1.
We avoided co-registration and co-normalization procedures (which use the same normalization parameters for both the pre- and post-images) of pre- and post-images, including registration of mean images to pre- and post-images, because of concerns of possible bias or problems occurring when structural properties were substantially different between pre- and post-images (Thomas and Baker 2012).
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This is convenient if we have several datasets and they should all be normalized using the same normalization factors.
BOLD image data of N-back fMRI tasks were co-registered to diffusion data, as described previously (Takeuchi et al. 2011c), and then normalized using the same normalization parameter as that used for diffusion data.
For this reason we used the same normalization procedure on all raw two-color array data.
Data obtained from the FLS cultures were similarly analyzed on Genespring®, using the same normalization steps and statistical tests.
Furthermore, to avoid artefacts arising from different normalization techniques, the raw data from these two datasets were pre-processed using the same normalization strategy.
The main function gcRMA converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as RMA (Robust Multiarray Average).
Corresponding Drosophila organs analyzed on a similar array platform using the same normalization procedure, found similar levels of relative gene activity.
We used the same normalization and analysis methods to minimize bias while further investigating the cause of qualitative and quantitative differences between RNA-Seq and Agilent oligonucleotide microarrays.
Figure 4 shows a scatter plot of relative CBF values measured with MRI-ASL and DCS during a representative stepped hypercapnia experiment, using the same normalization reference as the previous section.
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