What are the expression value of genes/probes in limma results of topTable
1
0
Entering edit mode
rkp • 0
@rkp-10175
Last seen 6.8 years ago

Dear All,

Kindly suggest me which value are expression value in the following table that can be utilized for plotting Heatmap.

     logFC   AveExpr         t      P.Value    adj.P.Val        B
  -6.828181  7.966478 -18.82087 5.665531e-14 5.032385e-10 21.33399
  4.855277 10.119313  18.69994 6.384443e-14 5.032385e-10 21.23390
-3.855238  9.043565 -18.66360 6.618656e-14 5.032385e-10 21.20367
-6.228212  4.886173 -17.73280 1.702977e-13 9.711228e-10 20.40300
-8.334742  8.435286 -16.80577 4.565306e-13 2.082693e-09 19.55247
-6.687395  6.121391 -16.62751 5.548775e-13 2.109459e-09 19.38246
-4.079570 10.274357 -16.09434 1.005614e-12 3.276864e-09 18.86092
 -6.300424  7.211431 -15.17983 2.904778e-12 7.504834e-09 17.91840
 -5.222531  6.654759 -15.16368 2.961136e-12 7.504834e-09 17.90119
-7.688590  9.899726 -14.68290 5.290129e-12 1.206678e-08 17.37925

 

Thanks in Advance

Heatmap • 1.1k views
ADD COMMENT
0
Entering edit mode

You normally use the normalised matrix and select probes/genes of interest from a statistical test, unless the variance in your data is very strongly related to your variables of interest - in this case you would use the most variables probes/genes and cluster these. I find aheatmap from the NMF package particularly good for this.
 

ADD REPLY
1
Entering edit mode
Aaron Lun ★ 28k
@alun
Last seen 3 hours ago
The city by the bay

None of the above. There's not much point making a heatmap from a single set of values - see the discussion at A: Heatmaps with replicates or triplicate data sets with counts to EdgeR, DESeq, or. If you want to make a heatmap, I would suggest using the original matrix of expression values. If you're using a one-way layout without an intercept, you could also use the fit$coefficients to visualise the average expression of each group (assuming you have more than two groups, otherwise the heatmap would be fairly boring).

ADD COMMENT

Login before adding your answer.

Traffic: 539 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6