Dear Galaxy community,
I’am new to the Galaxy project. I tried using the Volcano plot tool. Everytime I got th efollowing error message: [1] “Header row detected”
Error in log10(pvalue) : non-numeric argument to mathematical function
Calls: print … → f → sca
Does anybody knows what to do? I’am not familiar with bioinformatics or programming and really do not know what to do.
Thanks in advance.
CS
Dear @CSm,
Your input-file contains a header line, which might break the tool. You can remove the header line with " Remove beginning of a file".
Kind regards,
Florian
Dear Florian,
thank you very much for your reply. I tried already and removed the first line in the file, but the result is almost the same. Error message: Error in log10(pvalue) : non-numeric argument to mathematical function
Calls: print … → f → scales_add_defaults → lapply → FUN
Best regards
CS
Dear @CSm,
Please check if your inut file is correclty formatted. I assume that one or multiple lines (pvalues) are empty or contain NaN, Inf, or something else, which cannot be applied to a mathematical function, such as, log10.
Cheers,
Florian
Dear Florian,
thank you very much for your help. I checked already all lines for all parameter, but there are numbers only. From that point of view, it should be fine.
Best regards
CSm
Can you share your history? Then I could take a brief look.
Of course I can. Here it is: Galaxy | Europe | Accessible History | hPASMC Volcano plot
There are different files I tested with. Some are with and some are without header. Thank you very much for your help.
Best regards
CSm
It looks like you have numbers for your p-values, but from a programming standpoint, you do not have. Your p-values columns contain “values”, such as, “3,22212E-15”, which will be converted into a factor or string in R. Your values contain commas, which is not a float/double notation.
You have to save your table in a numeric format.
Kind regards,
Florian
Dear Florian,
thank you very much for your advice. Is it like in the history number 20 what you mean? The “3,22212E-15” format looks like in the training material for the volcano plot. Or do you think I have to substitute the comma by point?
Best regards
CSm
Or do you think I have to substitute the comma by point?
Yes
Dear Galaxy community,
I tried using the Volcano plot tool. Everytime I got th efollowing error message: [1] “Header row detected”
Error in log10(pvalue) : non-numeric argument to mathematical function
Calls: print … → f → sca
Does anybody knows what to do? My database looks like the picture.
Thanks in advance.
PS
Did you apply the adjustments that @Flow suggested? The screenshot shows those are not done yet.
