Question: How to plot Z-scores in R for gene expression data
0
gravatar for pixie@bioinfo
11 weeks ago by
pixie@bioinfo1.2k
India
pixie@bioinfo1.2k 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 • 311 views
ADD COMMENTlink modified 11 weeks ago by rice.researcher80 • written 11 weeks ago by pixie@bioinfo1.2k
3
gravatar for rice.researcher
11 weeks ago by
Korea, Republic Of
rice.researcher80 wrote:

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

ADD COMMENTlink written 11 weeks ago by rice.researcher80

Thanks, am looking into it.

ADD REPLYlink written 11 weeks ago by pixie@bioinfo1.2k

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 11 weeks ago by pixie@bioinfo1.2k
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 11 weeks ago by rice.researcher80

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

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by pixie@bioinfo1.2k
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