Common Mistakes

 This guide explains several common issues noted by our editors at each stage of the publishing process. Avoiding/addressing these kinds of mistakes before submitting will make things easier for you in that you will get less extraneous comments and more high-level feedback on your science. 

1.  Senior author missing. All manuscripts at eiRxiv are required to have a senior author. More information is provided on our Author Eligibility and Information page.
2. Inclusion of previously published figures. Figures that have been previously published cannot be used in your manuscript unless you have written permission from the author of the figure and the place of previous publication due to copyright reasons. If you feel that a previously published figure is absolutely essential to your manuscript please contact our editorial team where we will work with you to determine if the figure is necessary to include and provide guidance on the process of getting approval.
3. Manuscript is written like a lab report. One of the hardest things is transforming your work from a standard lab report format into a polished manuscript for publication! Our review process is aimed at helping our student authors with this, but here are some tips and tricks to help get you started:
   1. Use our manuscript template as you write your manuscript!
      1. We developed this template to specifically help our authors during the writing process and give examples of common mistakes in various sections of a manuscript.
   2. Look at previously published manuscripts at eiRxiv.
      1. We have hundreds of manuscripts online that you can look through! You can search by topic to find manuscripts related to your field of research as you’ll see that there are slight differences between different fields.
4. Formatted for publication already. Manuscripts submitted to us should not be formatted like the final posted PDFs you see of our articles. This formatting is done by our editors once the entire review process has been completed. Please use our manuscript template instead.
   This means that you should not use two-column formatting, font colors besides black, or place your figures directly in the results section of your manuscript (figures should still appear at the very end of your Word file above their caption).

1.  Lack of or inappropriate use of statistics. Statistics is a very complicated field, and even professional researchers struggle to apply the proper statistical tests to their data. eiRxiv also recognizes that access to professional statistical software can be a limitation for many students, but there are some statistical tests that can be run in Excel or even calculated by hand. We provide links to free online calculators in our stats guide. Statistical analysis is a very important tool in science because results of this analysis indicates the probability that the data observed happened by chance (a low probability or p-value indicates a “significant” result). Most eiRxiv studies include experiments following one of these patterns, in order of complexity:
   1. Comparing two groups (control and treatment) by a single dependent variable. This is a simple analysis requiring only a t-test.
   2. Comparing three or more groups by a single dependent variable.
      • i. Straightforward method: Ideally, this kind of data would be analyzed using a one-way ANOVA. If the ANOVA is significant, this can be followed by post hoc tests (Tukey and Dunnett’s tests are the most common) to look for differences between specific groups.
      • ii. Alternative method: If statistical software is a limitation, an ANOVA may be difficult, so you can alternatively analyze this type of data with t-tests. However, there is an important caveat: if you use multiple t-tests to compare related data, you increase the probability that you will find a statistically significant result among your comparisons by chance. Thus, a correction for multiple comparisons, such as a Bonferroni correction, is necessary. This correction basically reduces the alpha level or the threshold for a significant p-value.
   3. Comparing multiple groups by multiple dependent variables. This is somewhat complicated, but the best way to analyze this kind of data is by a multivariate ANOVA, again with post hoc tests. This will also indicate whether there are interaction effects between two variables (whether the effect of one variable is impacted by another variable).
2. Gene vs. protein nomenclature. Efforts have been made to standardize naming conventions for genes and proteins across different species so that they follow the same general format. Our editors will help verify that everything is correct, but these basics will help get you started.
   1. Genes are italicized. Whenever you write out a gene name (i.e. BRCA2) it should be italicized to denote that you are talking about the gene and not the protein.
      • i. This formatting also means that you don’t have to say “the BRCA2 gene” because the italics already tell your readers that it’s a gene.
   2. Proteins have no special formatting. Proteins don’t need any special formatting. You simply just write it out like BRCA2.
   3. Different species have different capitalization standards.
      • i. Human
        1. 1. For genes and proteins in humans every letter is capitalized in both the protein and gene names.
        2. 2. Gene: BRCA2
        3. 3. Protein: BRCA2
      • ii. Mouse, Rat, Zebrafish
        1. 1. Only the first letter is capitalized.
        2. 2. Gene: Brca2
        3. 3. Protein: Brca2
3. Species nomenclature. As with genes and proteins the scientific community has standardized the ways in which we write out the scientific names for organisms. When we talk about an organism, let’s say the common house mouse, we would first introduce it as Mus musculus. In this case you can see that both the genus and species names are italicized and the genus starts with a capital letter regardless if it starts a sentence. You only have to type out this full name the first time. After that you can simply just write “M. musculus” and it will be understood what you are referring back to.

1.   Tables labeled as figures. Many authors submit tables as images and refer to them as figures. However, tables (numbers organized in columns and rows) should be placed at the end of the Word document with the figure and table captions, and these should be editable in Word, not just pasted images of a table copied from another application. This allows the editors to edit and make comments on them. Tables should also be labeled as Table 1, Table 2, etc., which is a separate numbering system from the figures. Similar to figures, however, tables should also have a descriptive caption explaining what is shown and defining any abbreviations used in the table.
2. Figures and captions. Almost every manuscript that comes through copy editing receives suggestions for improving their figures and tables. This guide on making figures and tables for publication covers the major concerns.
3. Passive voice/tense used outside of the methods section. Passive voice or tense (e.g. The experiment was done at the school.) tends to be wordy and at times difficult to understand, in part because it can hide the subject of the sentence, so eiRxiv and many academic journals prefer the use of active voice (e.g. We did the experiment at the school.). The methods section is the only component of the manuscript where passive voice is acceptable.
4. Use of present tense to describe results. Everything that you did for your study was done in the past, and anything you did and any observations you drew should be written in past tense. The same goes for describing studies from the literature.
5. Improper acronym usage. Acronyms and abbreviations are useful tools for making your writing more concise, but to use them, please follow these guidelines:
   1. Spell out the entire word/phrase the first time the term is used followed by the abbreviation in parentheses. Example: “We used nuclear magnetic resonance (NMR) spectroscopy to validate our compound synthesis.”
   2. Once you define an acronym or abbreviation, use the abbreviation consistently throughout the rest of the manuscript unless use of the abbreviation would cause confusion.
6. Use of first-person singular (I, me). The only time first-person singular is acceptable in scientific writing is if a single author did the work and wrote the paper, and this is very rare. Every eiRxiv manuscript should have at least two authors, so even if you personally did the experiments, everything should be explained in terms of “we”.
7. References. The individual references in the references section should be formatted following eiRxiv’s modified MLA8 format. Please see our Reference Formatting page for more information and examples.

1.  Figures are low resolution. Figures should be of high enough resolution that they remain clear when scaled up or down in size. If your figure is not easily readable in the Word file of your manuscript, it will show up grainy in the final PDF of your manuscript. Figures tend to size down well, but rarely size up nicely; so, we always recommended erring on the side of saving your picture too big rather than too small. Please make sure you are saving your figures as images (JPEG, PNG, or TIFF) and not just taking screenshots of them!
2. Tables submitted as images. Tables need to be editable and located at the end of your Word file. Our proofing editors will help edit tables so they show up clearly in the final PDF. To do this they need to be able to easily change the cell size and spacing!
3. Equation formatting. We have more information about equation formatting in our “Equation Guide” found in our Author Resources.