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I very recently submitted a manuscript to a journal and found that I had mislabeled y axis on three panels of a many panel figure (put relative activity (%), instead of fold change in phosphorylation). Additionally I noticed that instead of PIP2, I put PIP3 in a signaling schematic. do you think the paper will be rejected for such errors if all other things are okay?

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    You paper will not be rejected just because of typos and misprints. – Alexey B. Jul 13 '16 at 19:18
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I agree with @Alexey B. and believe that, unless the typo has a very negative effect on the logical foundations of your paper, it will not cause the rejection of your paper.

Also, usually, you can contact the support staff of your journal and ask them if they can help you fix the issue. I made a rather similar mistake in a chart in one of my papers and for that, I contacted the support staff of the journal (published by Elsevier). After discussing the matter with them, they asked for the correct version of the chart, asked the editor of the journal if a modification is allowed and modified my submission.

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The correct course of action will be to e-mail the editor, outlining the typos and providing corrections. You should note that the typos have no influence on the conclusions or any other significant parts of the article.

You should do this as soon as possible, so the reviewers are also made aware of this. Assuming that your article doesn't get accepted right away with no changes required, you will have a chance to correct the errors in a later revision.

The worst thing to do would be to do nothing, or doing it too late. One thing that you do not want to do to have the article published with the errors in it. You have two options then, either ignore it and let the errors exist forever in the scientific record (worst option) or submit a correction which will be published as a separate article and will be referred to from the original article. Some publishers will actually correct the original article, but there's no guarantee this will happen. Either way, it's better to make the corrections as soon as possible. Which is now.

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