Question: Create a heatmap
0
gravatar for Morteza Hadizadeh
12 months ago by
Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
Morteza Hadizadeh30 wrote:

Hi every one,

I have an expression matrix that contains 20 rows (20 genes) and 435 columns (435 samples), all columns represent seven stages of a disease, I want to create a heatmap between genes and each stage. can I convert multiple columns to one column by averaging? In other words, convert the columns of each stage into one column by averaging.

I would be very pleased if you could guide me.

R • 306 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by Morteza Hadizadeh30
1

You can combine the columns how you like as long that it makes sense. For example, averaging doesn't make much sense if the underlying distribution of the data is multimodal or heavily skewed.

ADD REPLYlink written 12 months ago by Jean-Karim Heriche24k

Yes you can do this. But if you have analysed the data using something like limma or edgeR, then your differential expression pipeline might already have computed the treatment means. You might be able to skip your averaging step and use precomputed results.

ADD REPLYlink written 12 months ago by russhh5.5k
0
gravatar for H.Hasani
12 months ago by
H.Hasani980
Freiburg, Germany
H.Hasani980 wrote:

why don't you annotate them using ComplexHeatmap? if you wanted to average over the stages then I wouldn't use heatmap for it, probably a boxplot with the different categories on one axis and the distribution of gene expression on the second axis.

hth

ADD COMMENTlink modified 12 months ago • written 12 months ago by H.Hasani980
0
gravatar for Morteza Hadizadeh
12 months ago by
Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
Morteza Hadizadeh30 wrote:

I am sorry for the delay in replying, Thanks so much for your valuable answers.

ADD COMMENTlink written 12 months ago by Morteza Hadizadeh30
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