Blog Archives

Reproducible Research: Write your Clinical Chemistry paper using R Markdown

February 4, 2018
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Reproducible Research: Write your Clinical Chemistry paper using R Markdown

Abstract Background: This blog post is going to show you how to write a reproducible article in the field of clinical chemistry using R Mardkown. The only thing that will change for journal to journal will be the reference fomating and perhaps section numbering. The source code itself will be provided so that you can … Continue reading Reproducible...

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Mining Your Routine Data for Reference Intervals: Hoffman, Bhattacharya and Maximum Likelihood

September 5, 2017
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Mining Your Routine Data for Reference Intervals: Hoffman, Bhattacharya and Maximum Likelihood

Background Let me preface this by saying I am not making a recommendation to use the Hoffman method. Neither am I advocating for reference interval mining from routine data. There are many challenges associated with this kind of effort. That's for another post I think. However, I am going to how one does the calculations … Continue reading Mining...

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Non-Linear Regression: Application to Monoclonal Peak Integration in Serum Protein Electrophoresis

August 28, 2017
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Non-Linear Regression: Application to Monoclonal Peak Integration in Serum Protein Electrophoresis

Background At the AACC meeting recently, there was an enthusiastic discussion of standardization of reporting for serum protein electrophoresis (SPEP) presented by a working group headed up by Dr. Chris McCudden and Dr. Ron Booth, both of the University of Ottawa. One of the discussions pertained to how monoclonal bands, especially small ones, should be … Continue reading Non-Linear...

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Compare Tube Types with R – Repeated Measures ANOVA

August 21, 2017
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Compare Tube Types with R – Repeated Measures ANOVA

Background Sometimes we might want to compare three or four tube types for a particular analyte on a group of patients or we might want to see if a particular analyte is stable over time in aliqioted samples. In these experiments are essentially doing the multivariable analogue of the paired t-test. In the tube-type experiment, … Continue reading Compare...

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Parse an Online Table into an R Dataframe – Westgard’s Biological Variation Database

August 14, 2017
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Background From time to time I have wanted to bring an online table into an R dataframe. While in principle, the data can be cut and paste into Excel, sometimes the table is very large and sometimes the columns get goofed up in the process. Fortunately, there are a number of R tools for accomplishing … Continue reading Parse...

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Determine the CV of a Calculated Lab Reportable – Bioavailable Testosterone

August 7, 2017
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Determine the CV of a Calculated Lab Reportable – Bioavailable Testosterone

Background At the AACC meeting last week, some of my friends were bugging me that I had not made a blog post in 10 months. Without getting into it too much, let's just say I can blame Cerner. Thanks also to a prod from a friend, here is an approach to a fairly common problem. … Continue reading Determine...

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Conditional Formatting of a Table in R

November 7, 2016
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Conditional Formatting of a Table in R

Background There are a few ways to approach the problem of a conditionally formatted table in R. You can use the ReporteRs package's FlexTable() function, the formattable package, or the condformat package. These allow you to produce a conditionally formatted tables in HTML. You can also use xtable package and essentially program what you want … Continue reading Conditional...

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Make Easy Heatmaps to Visualize your Turnaround Times

September 8, 2016
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Make Easy Heatmaps to Visualize your Turnaround Times

The Problem In two previous posts, I discussed visualizing your turnaround times (TATs). These posts are here and here. One other nice way to visualize your TAT is by means of a heatmap. In particular, we would like to look at the TAT for every hour of the week in a single figure. This manner … Continue reading Make...

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Make Bland Altman Plots with Marginal Histograms using ggExtra

August 29, 2016
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The Problem As you know in Clinical Chemistry, we are not always writing a major paper but sometimes just preparing a short-report to answer a technical question that we've encounted at work. For shorter papers, journals often have more stringent rules about how many figures you can submit and even sometimes forbid multipanelled figures. In … Continue reading Make...

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A Shiny App for Passing Bablok and Deming Regression

August 15, 2016
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A Shiny App for Passing Bablok and Deming Regression

Background Back in 2011 I was not aware of any tool in R for Passing Bablok (PB) regression, a form of robust regression described in a series of three papers in Clinical Chemistry and Laboratory Medicine (then J Clin Chem and Biochem) available here, here and here. For reasons that are not entirely clear to … Continue reading A...

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