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Question: extracting the genes associated with the groups or samples in pheatmap.
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gravatar for morteza.hadizade
7 weeks ago by
morteza.hadizade10 wrote:

Hi everyone

I have an expression matrix, the rows contain 995 significant genes and columns contain 73 sample (995*73), samples are divided into 4 groups, after generation of heat map (pheatmap) from this matrix, how can I extract the genes associated with the groups or any sample?

I would be very pleased if you could guide me.

ADD COMMENTlink modified 7 weeks ago by Malcolm Cook1.5k • written 7 weeks ago by morteza.hadizade10

Hello Morteza,

You said in your question that you have determined the genes that are significant. Which package did you use to determine that? If you use limma, then its user guide will surely benefit you.

However, I get the feeling that what you have got so far is only the expression matrix.

ADD REPLYlink written 7 weeks ago by mikhael.manurung10

Hi,

Thank you for pointing this out. these genes are reported in an article, I get those from a supplementary file, I want to compare the genes of each group with my results. The gene list published in the supplementary file was a matrix, I clustered it by creating a pheatmap, but I could not extract the genes associated among each group or sample.

ADD REPLYlink written 7 weeks ago by morteza.hadizade10
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gravatar for Malcolm Cook
7 weeks ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:

You want to use cutree. Nice presentation at Question: extract dendrogram cluster from pheatmap

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Malcolm Cook1.5k

Thank you for linking to my answer on Biostars, Malcolm!

ADD REPLYlink written 7 weeks ago by Kevin Blighe10

Hi Kevin,

Thank you so much, your answer was reasonable and accurate.

According to your guidance, If I want to extract a gene list, I should use the cutree command, in this command, can I use the sample number instead of the cluster number?

I have 73 sample.

 

 

ADD REPLYlink written 6 weeks ago by morteza.hadizade10

Dear Malcolm,

Thank you I really appreciate your help.

ADD REPLYlink written 6 weeks ago by morteza.hadizade10
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