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Gender and hospital distribution of samples for case and control groups on both Phases is shown on (Additional file 1: Table S1).
In contrast to studies based on unpaired data (independent patient samples for case and control), paired data experiments have not been extensively applied in feature selection of transcriptome studies aiming to biomarker identification [ 9, 25, 26].
The ability to adjust samples for case mix is particularly topical in view of the recent National Joint Registry introduction of Patient Reported Outcome Measures for total knee replacement.
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These findings underscore the need for carefully matching samples, for example cases and controls, between geographical regions and highlight the need for replication in independent datasets.
DNA from archival patient HGSOC samples for cases #48 and #169 revealed homozygous BRCA1 methylation in chemotherapy-naive ascites collected at diagnosis for both cases and also in the surgical debulking samples following neoadjuvant chemotherapy for both cases (Supplementary Data 4).
Blood samples for cases were collected from patients within eight weeks of the first biopsy-proven lung cancer diagnosis and prior to removal of the tumor by a surgical procedure.
The post-treatment serum samples for cases 18 and 19 were lost in the clinic.
Genomic DNA was obtained from frozen whole blood samples for cases and controls in UCL1 and from saliva samples for the cases in UCL2.
DNA samples for cases and controls were grouped into pairs to minimize the effect of day-to-day laboratory variation.
Following the procedure described in Materials and Methods, we simulated samples for cases and controls in a 200-kb region.
These comprise non-representative samples of controls (e.g. other patients) and non-equivalent biological samples for cases and controls ([ 7]).
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