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Recent Replies

Comment: scatterplot in R
by
Asaf
9.3k

Compute it using all the expression values in the population (samples in each tumor type I assume). You will end up with one value for each…

Answer: antismash error
by
kblin
▴
30

Hi there, sorry for the late reply. I don't seem to get notification emails here on Biostars.
You'd run your FASTA file like:
```
anti…

Comment: scatterplot in R
by
bioinformatics
▴
10

Ok thanks for your help. How might I correctly calculate the SD?

Comment: scatterplot in R
by
Asaf
9.3k

You're misusing this formula. STDEV.S is for estimating the standard deviation of a population. What you are computing is basically the dis…

Answer: antismash download databases issue.
by
kblin
▴
30

The script should install the databases into the database directory. By default, this is in your antiSMASH install location. You can howeve…

Comment: scatterplot in R
by
bioinformatics
▴
10

The sd of an individual point is how spread the point/expression value of the gene in the sample is from the mean expression of all the sam…

Comment: scatterplot in R
by
Asaf
9.3k

What is the meaning of `sd` for an individual point? SD is relevant when considering a population. You can compute the mean and SD of the p…

Comment: scatterplot in R
by
bioinformatics
▴
10

In response to this comment:
You got a bit of a mess here. First of all you switched the parameters Samples and Expression.value, Samples …

Comment: scatterplot in R
by
Asaf
9.3k

You got a bit of a mess here. First of all you switched the parameters Samples and Expression.value, Samples should be on the X (first para…

Comment: scatterplot in R
by
bioinformatics
▴
10

I have used this command:
TIMP1Plot <- ggplot(df, aes(Expression.value, Samples, colour = Tumour.type)) + geom_point() + geom_errorbar…

Comment: scatterplot in R
by
bioinformatics
▴
10

I have tried this command with the columns mean and sd
TIMP1Plot <- ggplot(df, aes(Expression.value, Samples, colour = Tumour.type)) + …

Comment: identification of overlapped, proximal and distal gene for peak regions
by
husensofteng
▴
380

[BedTools window][1] could be useful here
[1]: https://bedtools.readthedocs.io/en/latest/content/tools/window.html

Comment: scatterplot in R
by
Asaf
9.3k

Sorry, I didn't read you question through. You should have columns in `df` named `mean` and `sd` for the expression in `geom_errorbar` to b…

Comment: scatterplot in R
by
bioinformatics
▴
10

Ok thanks, I have now done this however the error bar appeared on the legend not points. If I wanted to add an error bar for each point on …

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