Heatmaps for differential expressed probes

Question

[gs000095]

Dear all,

I processed raw methylation data using minfi and methylation array analysis libraries and finally came to a point that after I fit my model I get the up and down-regulated probes between different subgroups of my cancer.

``` fit2 <- contrasts.fit(fit,contmatrix)
     fit2 <- eBayes(fit2)
    #Number of Differentially methylated CpG sites at FDR 5%
    a1 <- summary(decideTests(fit2))

This gives an output of probes that are up or down-regulated in my 5 different subgroups as follows output

Now my question is, how can I extract all these differentially expressed probes? Can I use them directly to plot a heatmap or are there some other steps that need to be carried out? I tried using topTable() and it gave out all the probes arranged with the most significant p-values, however, when I try to plot the top 10 or 100 probes I get a memory error from the heatmap. Any help will be greatly appreciated!

Thank you in advance

Shweta

[cpad0112]

heatmap for differential expressed genes

https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/

For multiple coefficients: https://rforbiochemists.blogspot.com/2016/03/gene-expression-analysis-and_7.html

[gs000095]

Thank you so much for your feedback!