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Question: Possible construction of heatmap for clustering only genes for different treatments and not samples
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gravatar for svlachavas
2.4 years ago by
svlachavas570
Greece/Athens/National Hellenic Research Foundation
svlachavas570 wrote:

Dear Bioconductor Community,

from my analysis of an illumina microarray dataset (https://support.bioconductor.org/p/68307/#69270), i have acquired 5 DEG gene lists representing unique genes found DE between each specific biological treatment implemented vs the control group(DMSO). As i want to perform some unsupervised machine learning such as clustering and a possible heatmap of the intensities of these genes, im wondering how i should proceed based on the fact that are 5 contrasts:

One possible way i thought, is to subset from each contrast the top10 genes by abs(logFC), and then perform a heatmap with a clustering only on the rows(i.e genes) to identify genes that are similarly regulated, and/or possibly detect groups of genes that clustered together and thus regulated in a similar way across different treatments(possibly via heatmap.2). Or my cutoff is too arbitary and i could not possibly identify any significant patterns ?

Or alternatively should i intersect somehow the 5 DEG lists based on common probeIDs, and then use the common of all the contrasts to perform a heatmap only on these genes and only the treatments as samples for the visualization ?

Any recomendations, help or suggestions would be essential !!

Best,

Efstathios

ADD COMMENTlink modified 2.4 years ago by James W. MacDonald45k • written 2.4 years ago by svlachavas570
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gravatar for James W. MacDonald
2.4 years ago by
United States
James W. MacDonald45k wrote:

This question has nothing to do with how to do something using R/BioC, and everything to do with the best way to present results to show an interesting aspect of your data. The former is something that we can help you with, but the latter is something you have to discuss with your collaborators. How you present results is part of the art of science, and expecting people who know nothing about your experiment to chime in with suggestions is not likely to be helpful.

ADD COMMENTlink written 2.4 years ago by James W. MacDonald45k

Dear Mr James MacDonald, thank you for your answer, but my initial purpose was to include the link in which i analyze the puprose of my experiment, in order not to disturb people and have also a huge threat. I understand that each specific experiment design and interprentation has its own and unique questions to answer and results to present in different aspects-so, if still i have not described well my final goals:in summary i have acquired my 5 DEG lists which represent DEG genes found in each treatment implemented in my analysis, vs the control group DMSO. Thus, i would like to identify any possible common patterns(clusters-groups of genes) -and to present them in a heatmap- that behave similarly through any contrasts, or to detect any other significant patterns. That why i posted my question, because i would like some advice or suggestions how could i implement this in r(if there is a specific package or by heatmap.2) or generally any other idea of implementation

Thank you in advance !!

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by svlachavas570
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