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To avoid potential bias among the different genes in the datasets, duplicate rows and columns in the double-mutant fitness matrices were combined by calculating mean over the duplicates.
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In the kidney datasets, duplicates as well as individuals without gender assignments were excluded (Additional file 1: Table S1).
In our dataset, duplicate georeferenced specimens allowed efficient cleaning of our datasets, with c. 390 records deleted as a result.
We used datasets with duplicate measurements to test this.
All datasets contained duplicate measurements, either printed on the same array (breast cancer and lymphoma) or on separate arrays (melanoma, MEC).
In datasets with duplicates, the simplest possible correction is just a constant shift removing the bias found in duplicates where one measurement is sd (rd) while the other is known.
In our test, we used 100 sequences out of 260 because the original dataset contains duplicate sequences with different salt concentrations.
Each log-ratio dataset (from duplicate or triplicate samples) was used to identify TF-binding regions using the software (width of sliding window = 300 bp).
The contrast between the PMC citation dataset and the duplicate publication dataset shows that, whereas similarity in methods sections is generally more common than in other sections, similarity among results sections is the best indicator of a true duplicate publication.
The compounds were put together in one dataset and duplicated structures reported as being active against more than one target were removed in order to have unique active compounds on each target class.
Samples from dataset ST1 duplicated in dataset VDX were removed.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com