Hello - I'm new to the bioconductor suite and still don't quite understand how to invoke the exprs class. For example, let's say I'm trying to find genes within the ALL dataset with the most and the least significant effect on age. I've been able to write snippets to find the min/max exprs (expression level) within the set...
> min(exprs(ALL))
[1] 1.984919
> max(exprs(ALL))
[1] 14.12657
...but cannot seem to write a snippet that maps that min/max value to the actual gene?
As for assessing how age effects exprs, this is tricky. Each patient obviously has an age (which is a column) and also an expression level (which as I understand is a class) that maps back to a specific gene. As a start - I thought I'd just plot them but again I'm having trouble with the syntax, I've tried the following from what I've read on the web but to no avail...
> plot(exprs,age(ALL))
and...
> plot(exprs~age(ALL))
Error in age(ALL) : could not find function "age"
Anyone see a glaring problem?
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There is no glaring problem but an obvious one.
exprs(ALL)This returns a matrix.
minandmaxfunctions are returning the lowest and highest value from that matrix. I'm not sure ifagecolumn presents in a expressionSet object (my best guess is not). You just have columns - samples, rows-genes. If you want genes with highest effect on all samples, you may need to tryrowMeansfunction and take gene with highest mean across all samples and vice versa.May be you can add source from where you read it. Base
plotfunction can't handle the expressionSet.I don't think I understood how exactly you want to plot. Do you want to test correlation between age and gene expression?
Thanks venu - "age" is listed as a column:
A concept that I cannot quite grasp is from the above command I can see all the column names, there are 21 total. However, when I perform the following command...
...I can see that I have 12625 genes (rows) and 128 patients (columns). Why don't I see 128 column names with
colnames(pData(ALL))command?Hello oars!
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This is a pure R question and the error mesage is quite self-explanatory. Please search StackOverflow.
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My question also revolves around the uniqueness of the exprs class within the Biocondictor suite. I was hoping that someone familiar with the Bioconductor suite would help offer some insights on how this class is best called using R.
exprs is not a class, it is a function. Lots can be learned reading R help, like
?exprs, or?pData.class(ALL)will tell you ALL is an ExpressionSet object, and?ExpressionSetwill show lots of information on how to access and manipulate ExpressionSet objects.Thanks h.mon, I'll try to keep these posts to StackOverflow (but they're so mean over there).