Question: limma decideTests results; how to get/sort most significant Genes?
0
gravatar for bi_Scholar
2.6 years ago by
bi_Scholar0
bi_Scholar0 wrote:

Hello,

I just started working with limma and so far followed the limma users-guide to recive a TestResults Object.
I've printed the results into a file using write.fit() and a question arose while looking at the data.

Say I was looking at differential expressed genes in samples X vs. Y.
From my understanding, the values in column Res.X-Y indicate significant differential expressed genes for given p-value and adjustment method, where for value 1, the gene is significantly more expressed in X etc..
 

Now, how do I sort those significant differentially expressed genes so my output ranges from most-significant to least-significant (within the as significant annotated ones).
Does it make sense to just sort by Coef.X-Y decreasing or p-value increasing?

Does it even make sense to treat as significant annotated genes differently?


I just started to deal with limma and (microarray data in general) during my current semester, so please go easy on me in case I missed something obvious.

Many thanks in advance!

limma decidetests • 447 views
ADD COMMENTlink modified 2.6 years ago by Axel Klenk920 • written 2.6 years ago by bi_Scholar0
Answer: limma decideTests results; how to get/sort most significant Genes?
1
gravatar for Axel Klenk
2.6 years ago by
Axel Klenk920
Switzerland
Axel Klenk920 wrote:

 

Hello,

simply continue following the user's guide until you find limma's topTable() function

and make sure to read its help page to learn how to sort your results.

HTH.

ADD COMMENTlink written 2.6 years ago by Axel Klenk920

Hey Alex,
I've checked out topTable() and it is indeed what I was looking for. However, what if I choose 'global' as a method for decideTests() ? From my understanding, the Significant Genes found by topTable() and decideTests() could vary in this case.
As topTable() ranks Genes by F-Statistics, could I simply sort the Genes in TestResults by F-statistics and thus get the same ranking as in topTable() ?
 

ADD REPLYlink written 2.6 years ago by bi_Scholar0

in topTable, you can also use the sort.by function

so assuming you were writing your code it would be something along the lines of:

topTable(fit, number = Inf, sort.by = 'P', ....)
ADD REPLYlink written 2.6 years ago by jayme.rickman0
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