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To avoid bias resulting from preprocessing, Reyal et al [6] restricted their studies to data sets generated with the same chip (Affymetrix HG-U133A) for which raw data were available, and re-processed all data sets prior to merging.
Then, using the ArrayExpress function, we created R objects from all datasets for which raw data were available.
For the same reasons, we have only collected datasets for which raw data were available so we could normalize and pre-process all of them together with the same method.
To develop the algorithms, we selected from the WHO Global Database on Child Growth and Malnutrition [ 9] nutritional surveys for which raw data were available for analysis using the WHO standards.
In a more recent study a meta-analysis of individual patient data from the randomised, double-blind, placebo-controlled trials of dexamethasone for bacterial meningitis in patients of all ages for which raw data were available was performed.
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We selected 2,145 sample hybridizations performed on the Affymetrix GeneChip Mouse Genome 430 2.0 Array which are available from the Gene Expression Omnibus (GEO) [14], [15] for which raw data was available from GEO.
The two data sets for which raw data were unavailable were excluded.
We considered only the datasets of which the raw data were available except for one case whose authors provided us kindly with their unpublished raw data.
Raw data were available for many of the original studies, allowing us to estimate average effect-sizes at some locations.
The raw data is available in Data S1.
Raw data are available in the authors' group, which can be provided if requested.
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