scholarly journals Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays

Epigenomics ◽  
2022 ◽  
Author(s):  
Ze Zhang ◽  
Min Kyung Lee ◽  
Laurent Perreard ◽  
Karl T Kelsey ◽  
Brock C Christensen ◽  
...  

Aim: Tandem bisulfite (BS) and oxidative bisulfite (oxBS) conversion on DNA followed by hybridization to Infinium HumanMethylation BeadChips allows nucleotide resolution of 5-hydroxymethylcytosine genome-wide. Here, the authors compared data quality acquired from BS-treated and oxBS-treated samples. Materials & methods: Raw BeadArray data from 417 pairs of samples across 12 independent datasets were included in the study. Probe call rates were compared between paired BS and oxBS treatments controlling for technical variables. Results: oxBS-treated samples had a significantly lower call-rate. Among technical variables, DNA-specific extraction kits performed better with higher call rates after oxBS conversion. Conclusion: The authors emphasize the importance of quality control during oxBS conversion to minimize information loss and recommend using a DNA-specific extraction kit for DNA extraction and an oxBSQC package for data preprocessing.

2010 ◽  
Vol 29 (22) ◽  
pp. 2347-2358 ◽  
Author(s):  
Helmut Finner ◽  
Klaus Strassburger ◽  
Iris M. Heid ◽  
Christian Herder ◽  
Wolfgang Rathmann ◽  
...  

2021 ◽  
Author(s):  
Francesco Battocchio ◽  
Jaijith Sreekantan ◽  
Arghad Arnaout ◽  
Abed Benaichouche ◽  
Juma Sulaiman Al Shamsi ◽  
...  

Abstract Drilling data quality is notoriously a challenge for any analytics application, due to complexity of the real-time data acquisition system which routinely generates: (i) Time related issues caused by irregular sampling, (ii) Channel related issues in terms of non-uniform names and units, missing or wrong values, and (iii) Depth related issues caused block position resets, and depth compensation (for floating rigs). On the other hand, artificial intelligence drilling applications typically require a consistent stream of high-quality data as an input for their algorithms, as well as for visualization. In this work we present an automated workflow enhanced by data driven techniques that resolves complex quality issues, harmonize sensor drilling data, and report the quality of the dataset to be used for advanced analytics. The approach proposes an automated data quality workflow which formalizes the characteristics, requirements and constraints of sensor data within the context of drilling operations. The workflow leverages machine learning algorithms, statistics, signal processing and rule-based engines for detection of data quality issues including error values, outliers, bias, drifts, noise, and missing values. Further, once data quality issues are classified, they are scored and treated on a context specific basis in order to recover the maximum volume of data while avoiding information loss. This results into a data quality and preparation engine that organizes drilling data for further advanced analytics, and reports the quality of the dataset through key performance indicators. This novel data processing workflow allowed to recover more than 90% of a drilling dataset made of 18 offshore wells, that otherwise could not be used for analytics. This was achieved by resolving specific issues including, resampling timeseries with gaps and different sampling rates, smart imputation of wrong/missing data while preserving consistency of dataset across all channels. Additional improvement would include recovering data values that felt outside a meaningful range because of sensor drifting or depth resets. The present work automates the end-to-end workflow for data quality control of drilling sensor data leveraging advanced Artificial Intelligence (AI) algorithms. It allows to detect and classify patterns of wrong/missing data, and to recover them through a context driven approach that prevents information loss. As a result, the maximum amount of data is recovered for artificial intelligence drilling applications. The workflow also enables optimal time synchronization of different sensors streaming data at different frequencies, within discontinuous time intervals.


2008 ◽  
Vol 13 (5) ◽  
pp. 363-377 ◽  
Author(s):  
Xiaohua Douglas Zhang

One of the most fundamental challenges in genome-wide RNA interference (RNAi) screens is to glean biological significance from mounds of data, which relies on the development and adoption of appropriate analytic methods and designs for quality control (QC) and hit selection. Currently, a Z-factor-based QC criterion is widely used to evaluate data quality. However, this criterion cannot take into account the fact that different positive controls may have different effect sizes and leads to inconsistent QC results in experiments with 2 or more positive controls with different effect sizes. In this study, based on a recently proposed parameter, strictly standardized mean difference (SSMD), novel QC criteria are constructed for evaluating data quality in genome-wide RNAi screens. Two good features of these novel criteria are: (1) SSMD has both clear original and probability meanings for evaluating the differentiation between positive and negative controls and hence the SSMD-based QC criteria have a solid probabilistic and statistical basis, and (2) these QC criteria obtain consistent QC results for multiple positive controls with different effect sizes. In addition, I propose multiple plate designs and the guidelines for using them in genome-wide RNAi screens. Finally, I provide strategies for using the SSMD-based QC criteria and effective plate design together to improve data quality. The novel SSMD-based QC criteria, effective plate designs, and related guidelines and strategies may greatly help to obtain high quality of data in genome-wide RNAi screens. ( Journal of Biomolecular Screening 2008:363-377)


Author(s):  
Antonella D. Pontoriero ◽  
Giovanna Nordio ◽  
Rubaida Easmin ◽  
Alessio Giacomel ◽  
Barbara Santangelo ◽  
...  

2014 ◽  
Vol 5 ◽  
Author(s):  
Shefali S. Verma ◽  
Mariza de Andrade ◽  
Gerard Tromp ◽  
Helena Kuivaniemi ◽  
Elizabeth Pugh ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document