Question: How to plot Z-scores in R for gene expression data
0
gravatar for pixie@bioinfo
9 months ago by
pixie@bioinfo1.3k
pixie@bioinfo1.3k wrote:

Hello, I have a table with gene expressions across samples. I have calculated the z scores and need to create this plot as given below: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022196#pone-0022196-g001

My table looks like:

Gene_name E_2401_ctrl_1 E_2401_ctrl_2 E_2401_ctrl_3 E_2401_drt_1 E_2401_drt_2 LOC_Os01g01312 1.601736731 0.310548148 1.238589942 -0.899941148 -0.980640435 LOC_Os01g01360 -0.850254449 -0.420792594 0.083358279 0.86759297 0.102030534 LOC_Os01g01390 0.40382069 -0.377555928 -0.009849284 -0.285629267 0.219967368 LOC_Os01g01610 -1.102507436 -0.90329537 -0.458899223 1.042853272 0.904937227 LOC_Os01g01620 -0.806239145 -1.190898502 -0.229250108 0.812535653 1.004865332

I have almost 3000 genes and 50 samples. Hence plotting in excel is not an option.

Kindly help

gene expression • 773 views
ADD COMMENTlink modified 5 months ago by guangguotan0 • written 9 months ago by pixie@bioinfo1.3k
3
gravatar for rice.researcher
9 months ago by
Korea, Republic Of
rice.researcher90 wrote:

You can use free software MultiExperiment Viewer (MeV) for generating the plot mentioned in the article. Documentation is available Here

ADD COMMENTlink written 9 months ago by rice.researcher90

Thanks, am looking into it.

ADD REPLYlink written 9 months ago by pixie@bioinfo1.3k

Actually, MultiExperiment Viewer (MeV) creates clusters and then we can visualize plots. Here, I have already clustered my data and wish to visualize

ADD REPLYlink written 9 months ago by pixie@bioinfo1.3k
1

Even without clustering, you can generate such image. For ex, in the left panel of MeV, go to Cluster manager->Gene clusters. Then you can find a drop down box (at left top) and select expression graph option.

ADD REPLYlink written 9 months ago by rice.researcher90

Thank you so much,I finally could do it. You saved a lot of time for me !

ADD REPLYlink modified 9 months ago • written 9 months ago by pixie@bioinfo1.3k
0
gravatar for guangguotan
5 months ago by
guangguotan0 wrote:

I encounter the same problem. how to solve the problem about ploting Z-scores? thank you very much!

ADD COMMENTlink written 5 months ago by guangguotan0
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