Differential analysis between A vs B gave me differential expressed genes like following:
Genes logFC unshrunk.logFC logCPM PValue FDR
Gene1 4.704568888 4.705411203 6.335398698 2.87E-45 5.68E-41
Gene2 5.046769012 5.048410913 5.713396847 6.54E-45 6.46E-41
Gene3 7.582765878 7.824749841 1.200751502 2.03E-43 1.33E-39
Gene4 4.326319082 4.328231859 4.779115389 1.28E-42 5.32E-39
Gene5 4.835955903 4.840334013 4.091127747 1.35E-42 5.32E-39
Gene6 5.312117056 5.314688138 5.331640406 1.98E-42 6.52E-39
Gene7 -5.76775 -5.7776037 4.209391248 5.25E-42 1.48E-38
Gene8 4.562730239 4.564646863 5.011354411 8.05E-42 1.99E-38
Gene9 4.571347719 4.573313339 4.982581445 1.61E-41 3.54E-38
Gene10 4.830679248 4.8340846 4.44951126 2.18E-40 4.31E-37
Gene11 8.263335175 8.279036992 5.679556644 8.20E-40 1.47E-36
Gene12 4.498284621 4.504950052 3.156431424 1.33E-39 2.19E-36
Gene13 10.08604587 10.31318144 3.689108577 1.79E-39 2.71E-36
Gene14 4.802704588 4.805611342 4.648881244 2.07E-39 2.92E-36
Gene15 4.299553259 4.303901316 3.574867745 3.12E-38 4.11E-35
Gene16 -9.0340898 -9.2400894 3.20071166 4.09E-38 5.05E-35
And Differential analysis between C & D gave:
Genes logFC unshrunk.logFC logCPM PValue FDR
Gene1 9.830763229 9.857045013 2.461083784 7.33E-15 1.57E-10
Gene18 8.314196291 8.315523973 5.262615028 2.86E-13 3.06E-09
Gene3 11.80447191 11.82477085 4.815575477 1.07E-12 7.60E-09
Gene2 -11.28982093 -11.30537113 8.063029358 3.48E-12 1.86E-08
Gene21 10.45942991 10.46806536 4.673637229 9.87E-12 4.22E-08
Gene22 8.444533948 8.446387311 4.908046624 9.49E-11 3.38E-07
Gene4 -8.36656005 -8.398162862 4.11782659 2.44E-10 6.20E-07
Gene24 -9.953626757 -9.986020817 5.625058944 2.61E-10 6.20E-07
Gene25 9.452210058 9.4636667 3.291139413 2.61E-10 6.20E-07
Gene6 9.609186353 9.615829541 4.213984617 3.39E-10 7.24E-07
Gene9 -8.337494271 -8.349468295 5.483300689 4.36E-10 8.47E-07
Gene28 -13.03662321 -144269487.5 3.249843933 4.97E-10 8.85E-07
Gene29 -10.26198778 -10.33006096 4.8776179 6.02E-10 9.89E-07
I want to make a scatter plot to look at their association. The scatterplot should look something like Figure 2a in this Research paper
You want to compare A vs B and C vs D using scatter plot?
I want to check their association. All the genes in the tables are both protein-coding and lncRNAs. I want to make a plot something like mentioned in the paper Figure 2a
Not clear, there is no overlap of genes between the two datasets. If that is how it is intended, then what do you expect x-axis and y-axis to be?
I made the changes in the table. There are few overlap genes between both datasets. x-axis (A vs B) y-axis (C vs D)
Merge on gene names then plot, something like:
plot(merge(AB[, 1:2], CD[, 1:2], by = "Genes")[, c(2, 3)])
ok. I did like this
But this showed only points on the plot not the gene names.
Try:
Biologist : Please do not delete posts that have received comments/answers. If you have managed to solve your problem then post your solution as an answer here so it can be useful for someone in future.
Sorry, I wanted to post the question with some update. So deleted it. Anyways I made some changes now. thank