# erros with Volcano plot : a lot of point in the top

**URL:** <https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654>\
**Category:** Uncategorized\
**Tags:** workflow\
**Created:** [September 9, 2021, 4:02pm UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654 "2021-09-09T16:02:37Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![azzahrae](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/azzahrae/32/2584_2.png) [@azzahrae](https://help.galaxyproject.org/u/azzahrae)\
**Post date:** [September 9, 2021, 4:02pm UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654/1 "2021-09-09T16:02:37Z")

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hello, I performed the differential analysis using the following pipeline, trimmomatic → kallisto quant → deseq . I get the volcano plot on the screen below using the volcano plot tool with Significance threshold = 0.05 .

![jk](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/8/8dd27997fa596444da8255af0d8d8a4284d6c510.png)

there is a lot of genes at the top, what’s wrong with it ? if it’s normal what’s the interpretation of it ?

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [September 13, 2021, 10:16am UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654/2 "2021-09-13T10:16:48Z")

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Hi @azzahrae,  
could you try to sort the DESEQ result file according to the p-values and share a screenshot of it? I think that the plot is fine, just those genes at the top are those whose p-value is extremely low.

Regards

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**Author:** ![azzahrae](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/azzahrae/32/2584_2.png) [@azzahrae](https://help.galaxyproject.org/u/azzahrae)\
**Post date:** [September 15, 2021, 6:29pm UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654/3 "2021-09-15T18:29:51Z")

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hi @gallardoalba, the attached field is the result of deseq without sort, there is some problem in the galaxy server I can’t do the sorting task.  
[deseq2 result](https://usegalaxy.org/datasets/bbd44e69cb8906b58d7fdca7a36b0525/display/?preview=True)

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [September 16, 2021, 7:14am UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654/4 "2021-09-16T07:14:58Z")

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Hi @azzahrae,  
it seems that some genes show such a low p-value that is considered as 0 (because the smallest floating-point value in R is 2.225074e-308, so anything smaller is rounded to 0), and the -log of a number tending to 0 is infinite.

Regards

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**Author:** ![azzahrae](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/azzahrae/32/2584_2.png) [@azzahrae](https://help.galaxyproject.org/u/azzahrae)\
**Post date:** [September 16, 2021, 8:28am UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654/5 "2021-09-16T08:28:35Z")

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thank you, what we can say about these genes as an interpretation?

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [September 16, 2021, 8:40am UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654/6 "2021-09-16T08:40:41Z")

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According to the DESeq2 results, you could hypothesize that those genes are the most relevant from a biological point of view (the ones whose differential expression is more significant from a statistical point of view). But anyway, I suggest you consider in the downstream steps all those genes whose Adjusted p-value is lower than 0.05.

Regards

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [September 16, 2021, 9:19am UTC](https://help.galaxyproject.org/t/erros-with-volcano-plot-a-lot-of-point-in-the-top/6654/7 "2021-09-16T09:19:14Z")

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Today is the [Galaxy Papercuts CoFest Day](https://galaxyproject.org/events/2021-09-papercuts/); if you are interested in getting in touch with the Galaxy community, it can be a good opportunity. Regards!