limma for GX data

Question

[shresh.stayintouch]

Hi

I am having one basic doubt.

I did my gene expression analysis using Illumina platform and data was analyzed in limma which gives me normalized and background substracted intensities,converted to log scale(log 2 intensities values)for both my control group and test group.I could identify DEG(differentially expressed genes) amongst the groups,suppose around 3000 genes.For identifying these genes the software groups my all test sample in 1 group and all control samples in 1 group and find a significant p value.When I go to generate the heat map ,mostly Fold changes values are used per sample.

Now do I have to calculate individual FC for every sample for generating heat map or does limma directly calculates FC

for plotting the heatmap?

[shresh.stayintouch]

It's not clear.See I have grouped my all 50 samples under 2 groups test and control for identifying DEG.So now I have a list of

DEG with there FC difference in 1 column .

Now how to plot heat map with just 2 coulmns(1 list of DEG and 1 their FC) for all the 50 sample.

[Devon Ryan]

What would be the point of a heatmap with just two columns? Just use the results table, it's more informative. Heatmaps are nice because you can get an overview of how samples cluster and how blocks of probes change together. With just two columns, you'd lose the variance information, which is quite important.

Answer 1

[Devon Ryan]

The heatmaps graph the absolute (or normalized) signal per probe per sample, so there's nothing for you to calculate there (after normalization and such with limma).