Question

extracting the genes associated with the groups or samples in pheatmap.

0

Entering edit mode

morteza.hadizade ▴ 10

@mortezahadizade-16792

Last seen 8 months ago

Iran

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.

R microarray • 2.5k views

ADD COMMENT • link updated 6.2 years ago by Malcolm Cook ★ 1.6k • written 6.2 years ago by morteza.hadizade ▴ 10

0

Entering edit mode

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 REPLY • link 6.2 years ago mikhael.manurung ▴ 280

0

Entering edit mode

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 REPLY • link 6.2 years ago morteza.hadizade ▴ 10

score 2 · Answer 1 · 2018-09-30

2

Entering edit mode

Malcolm Cook ★ 1.6k

@malcolm-cook-6293

Last seen 3 months ago

United States

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

ADD COMMENT • link 6.2 years ago Malcolm Cook ★ 1.6k

0

Entering edit mode

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

ADD REPLY • link 6.2 years ago Kevin Blighe ★ 4.0k

0

Entering edit mode

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 REPLY • link 6.1 years ago morteza.hadizade ▴ 10

0

Entering edit mode

Dear Malcolm,

Thank you I really appreciate your help.

ADD REPLY • link 6.1 years ago morteza.hadizade ▴ 10