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One in five genetics papers contains errors thanks to Excel (2016)

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Re: One in five genetics papers contains errors thanks to Excel (2016)

#31

Post by Prickle »

prepend wrote: post #15
monocasa wrote: post #7

Earlier quoted context omitted.

> One in five genetics papers contains errors because the authors were careless when using Excel Or Excel is a remarkably easy tool to mishandle because of generally unexpected transformations it makes 'for you' automatically in an easy to miss way.

You think Excel should make special accommodations because genetics authors misuse it? Excel has been acting this way since before bioinformatics existed. Authors need to use their tools properly.

They already did in 2023.

Excel did not have an option for turning automatic conversions off.

You can now, FINALLY disable automatic conversion. Honestly that "feature" has been a bane of my existence, and I don't work with genes.

Re: One in five genetics papers contains errors thanks to Excel (2016)

#33

Post by redbell »

Here's another interesting article on the same topic (2016) entitled "Gene name errors are widespread in the scientific literature" : https://genomebiology.biomedcentral.com/articles/10.1186/s13...

From the article:

"The problem of Excel software inadvertently converting gene symbols to dates and floating-point numbers was originally described in 2004. For example, gene symbols such as SEPT2 (Septin 2) and MARCH1 [Membrane-Associated Ring Finger (C3HC4) 1, E3 Ubiquitin Protein Ligase] are converted by default to ‘2-Sep’ and ‘1-Mar’, respectively."

Re: One in five genetics papers contains errors thanks to Excel (2016)

#34

Post by [deleted] »

prepend wrote: post #15
monocasa wrote: post #7

Earlier quoted context omitted.

> One in five genetics papers contains errors because the authors were careless when using Excel Or Excel is a remarkably easy tool to mishandle because of generally unexpected transformations it makes 'for you' automatically in an easy to miss way.

You think Excel should make special accommodations because genetics authors misuse it? Excel has been acting this way since before bioinformatics existed. Authors need to use their tools properly.

[deleted]

Re: One in five genetics papers contains errors thanks to Excel (2016)

#36

Post by freehorse »

At work we have had problems with excel changing values of numerical entries due to different locale formatting multiple times in the past, and many times causing hours of lost time till the culprit (excel) was found. Other types of values that are completely inconvenient for excel include social security numbers and phone numbers; which one would assume are more general purpose and thus closer to the standard use cases of excel than genes. Still excel is messing these things up. Opening a csv file is also a non-trivial overly complicated endeavour for excel in year 2024, which should be done with a double click (somehow other spreadsheet programs manage to handle csv files much more easily). The worst is that excel is usually used by non-technical people, who misunderstand these idiosyncrasies and time is wasted over and over.

Re: One in five genetics papers contains errors thanks to Excel (2016)

#37

Post by lukan »

hilbert42 wrote: post #35

Don't we ever learn. We've known since VisiCalc in the '80s not to trust spreadsheets for important data without crosschecking the results. The question is why do we still use substandard tools for processing important data like this.

"The question is why do we still use substandard tools for processing important data like this."

Because there is no better alternative (yet)?

A better alternative needs to be really better, to justify the effort of people relearning how to do things in this better tool then.

Re: One in five genetics papers contains errors thanks to Excel (2016)

#38

Post by lukan »

magicalhippo wrote: post #30

I use Excel a fair bit at work, mostly for looking at data, but also to fairly easily generate SQL statements based on such data, often after some formulas have been applied. Though I think what I'd really want is some tool which has the same grid-like visualization, filtering and direct entering, but was code-based under the hood and without magic conversions. So, take Excel, and when you enter a formula in a cell,…

Yes, something like this is on my mind since quite some years as well.

It would be limited to programmers, though.

Re: One in five genetics papers contains errors thanks to Excel (2016)

#39

Post by scrlk »

magicalhippo wrote: post #30

I use Excel a fair bit at work, mostly for looking at data, but also to fairly easily generate SQL statements based on such data, often after some formulas have been applied. Though I think what I'd really want is some tool which has the same grid-like visualization, filtering and direct entering, but was code-based under the hood and without magic conversions. So, take Excel, and when you enter a formula in a cell,…

The Data Wrangler extension for VS Code might be of interest. As you apply operations to your dataset, it generates Pandas code.

https://code.visualstudio.com/docs/datascience/data-wrangler

https://www.youtube.com/watch?v=5tWJVLF6PuA

Re: One in five genetics papers contains errors thanks to Excel (2016)

#40

Post by lukan »

saagarjha wrote: post #27
prepend wrote: post #18

Earlier quoted context omitted.

Excel is not a genetics tool. It has millions if use cases, many more important than genetics. Excel didn’t care about this. It’s like people complaining because sugar gets misused. Or that murderers stab people with knives. The solutions isn’t to “fix” knives.

Excel is a tool for general-purpose data processing. What the genetics people are doing is exactly that.

Also it is a somewhat working solution, to ban knives in certain places, like clubs, so people don't become drunk murderers in the first place ..
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