Question: (Closed) Scaling by individual row when plotting heatmap using DEseq2
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gravatar for aropri
3 months ago by
aropri50
aropri50 wrote:

Hi,

I am trying to create a heatmap of differentially expressed lncRNAs in normal, atypical, dcis, and invasive breast cancer patient samples. I have created a heatmap from the counts file but it creates a color map based of the counts of highest or lowest expressed RNAs not in that specific row but in general. So a specific lncRNA is expressed 100 times in cancer, but that lncRNA is only expressed 20 times in normal, it still shows blue as a color becausec some other lncRNA represented in a different row is expressed a 1000 times. I want to create a color map where the color coordinates to the expression of that specific RNA in that row across the different conditions. So a specific lncRNA is expressed 100 times in cancer, but that lncRNA is only expressed 20 times in normal, it should show red for cancer vs blue for normal. Basically, I want the scale or the heatmap be relative to each row across the four different conditions for one lncRNA. Any help is appreciated.

rna-seq • 132 views
ADD COMMENTlink written 3 months ago by aropri50

The heatmap scales on your data. What you need to do is to log10 scale the fold difference.

ADD REPLYlink written 3 months ago by _r_am31k

Hello aropri!

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ADD REPLYlink written 3 months ago by ATpoint42k
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