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Recent Replies
Comment: BLAST options error: File homo_ref.faa does not exist
by
logbio
▴
30
When I try what you said and run the makeblast command again, this time I get the following error. "`BLAST options error: homo_ref.faa does…
Comment: scatterplot in R
by
bioinformatics
▴
10
Ok thanks for your response. If the sd and mean values are not part of the table where should I put them?
Comment: scatterplot in R
by
Asaf
9.3k
Each row is one sample so the mean and sd should not be a part of the table. There are elegant ways to plot the mean and SD of a population…
Comment: scatterplot in R
by
bioinformatics
▴
10
Ok thanks. I have ended up with a mean value and sd for each population.
Is this table correct?
head(df)
Samples Expressi…
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…
Comment: 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)) + …
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