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Batch effects between datasets were adjusted for by the empirical Bayes method ComBat/SVA [ 32– 32].
To counteract overregularization and loss of detail in case of the attenuation CT, the noise power spectrum of the three mice datasets were adjusted by weighting iterative reconstruction and conventional filtered back-projection reconstruction (with Ram-Lak filter) with 0.75 and 0.25 respectively.
Finally, systemic non-biological interlaboratory experimental variation ("batch effect") between the datasets was adjusted using non-parametric empirical Bayes frameworks implemented in ComBat (http://statistics.byu.edu/johnson/ComBat) [18].
Each of the four microarray datasets was adjusted for estrogen and progesterone receptor (ER/PR) status as well as age to avoid their influence.
The phenotypes in this combined dataset were adjusted slightly from their original publications based on a more recent analysis of the Keio Collection genotypes [ 26].
To batch correct the gene expression data [ 21, 22], the probeset medians in each individual dataset were adjusted to the MDACC133 reference set accounting for differences in the proportion of clinical ER+ / − samples; after batch correction, all ER− tumors were removed, as were all ER+ tumors not treated with tamoxifen-only, thus leaving 594 tumors per microarrays.
The TCGA dataset was adjusted for age, FIGO stage and histologic grade, but not subtype because all the samples were of the serous subtype.
All data analyses were conducted using STATA version 11, and the dataset was adjusted for cluster sampling design and weighted appropriately.
Analysis of the combined dataset was adjusted for sample group (discovery/replication).
**The UK GWAS dataset was adjusted for age, FIGO stage, histologic subtype, grade and study site.
Operative time from procedures in the testing dataset was adjusted using models derived from the training dataset.
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