Background In a previous post I was toying with better ways to integrate monoclonal proteins by deconvolution of monoclonal peaks. Turns out this is a hard problem. In any case, Deep Learning Neural Networks have become so mature that I wanted to see how easy it is to identify the presence of monoclonal proteins in the gamma region from the densitometric scan. This is not a new idea as it was first suggested in 1992 in J. Clin Pathol by Kratzer et al. I have to say, that was a very cool idea but as far as I can tell, it has not gotten much traction. This paper is mostly cited by review article ..read more

Introduction This is the first of what I am hoping are a number of posts on different machine learning classifiers. The subject matter is not lab medicine but the methodology applies to any similar project. For example, maybe you want to classify the text of a general internal medicine consult into its subspecialty based on the words used or perhaps you want to determine which IT tickets are likely high priority. Maybe you want to convert free text diagnoses into categorical diagnoses. Ultimately, the problem I want to tackle is text classification. In any case, the book that I have been readi ..read more

My friend Patrick Mathias from the University of Washington Department of Laboratory Medicine gave a fantastic talk on MSACL Connect last week about using #rstats and other open source tools for data automation in COVID sample collection, accessioning, pooling and direct-to-patient reporting. Following his talk, I shared the details of our COVID sample pooling data automation strategy which is built on R, R Shiny and Ubuntu. Click here or on the image below to go to the talk on MSACL Connect.     “When he heard this, Jesus said, ‘This sickness will not end in death. No, it is for God ..read more

Background As part of our lab accreditation requirements, we have to provide measurement uncertianty estimates for all tests at all hospital sites. As you might imagine, with thousands of testcodes in Sunquest LIS, getting all the coefficients of variation (CVs) represents a daunting task for the quality technologist to accomplish. As it turns out, by capturing the ssh session in a .txt file, you can use R’s dplyr package to do this all in few lines of code. Getting the Raw Data You need to get the raw data from Sunquest. You can capture the telnet (yes… older versions of Sunquest use telnet a ..read more

Background R dogma is that for loops are bad because they are slow but this is not the case in C++. I had never programmed a line of C++ as of last week but my beloved firstborn started university last week and is enrolled in a C++ intro course, so I thought I would try to learn some and see if it would speed up Passing Bablok regression. Passing Bablok Regression As mentioned in the past, the field of Clinical Chemistry has a peculiar devotion to Passing Bablok regression… and hey, why not? Here is the code for a minimal implementation of Passing Bablok regression as discussed in this paper ..read more

MSACL Conference There are two RStats Data Science courses happening in Salzburg Austria on September 22–24, 2019 at the 6th annual MSACL Clinical Mass Spectrometry Conference. These courses are held twice annually, once in Europe and once in Palm Springs. Introductory Course The introductory course will be taught by Dan Holmes, MD of the University of British Columbia and Will Slade, PhD of Laboratory Corporation of America. Course description is here Intermediate/Advanced Course The intermediate/advance course will be taught by Shannon Haymond, PhD of Northwestern University and Patrick ..read more

Background I like writing my academic papers in RMarkdown because it allows reproducible research. The cleanest way to submit a manuscript made in RMarkdown is using the LaTeX code that it generates using the YAML switch keep_tex = true. A minimalist YAML header would look like so: --- title: The document title author: - Duke A Caboom, MD - Justin d'Ottawa, PhD: output: pdf_document: keep_tex: true --- Introduction However, when you want mutliple authors affiliations you discover that you can’t do as you would in LaTeX because Pandoc does not know what to do with the affiliations ..read more

Abstract Background: This blog post is going to show you how to write a reproducible article in the field of clinical chemistry using R Markdown. 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 use it as a template. Methods: The paper will use R, R-Markdown, bookdown and pandoc. The references will be taken care of using BibTeX and reference formatting will be managed with Zotero csl files. Results: The result will be a manuscript that anyone can reproduce. Conclusions ..read more

Background Let me preface this by saying I am not making a recommendation to use the Hoffmann 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 for two methods I have seen used: the Hoffmann Method and the Bhattacharya Method. Then I will show how to do this using the mixtools package in R which uses the expectation maximum algorithm to determine the maximum likelihood. The Concept When you look at histograms of rout ..read more

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 integrated. While many use the default manual vertical gating or “drop” method offered by Sebia's Phoresis software, Dr. David Keren was discussing the value of tangent skimming as a more repeatable and effective means of monoclonal protein qua ..read more