How to calculate combined expression of two genes
0
0
Entering edit mode
3.1 years ago

Hi,

I am trying to calculate the combined expression of two genes. I'm not entirely sure even where to begin with this. I have a list of cohorts that I obtained from a public database. I took the median RSEM normalized expression for each of the two genes and create a table that I will add below. I was just wondering how I can calculate the combined expression for these two genes? Let me know if you need any more detail.

test <- structure(list(cohort = c("ACC", "BLCA", "BRCA", "CESC", "CHOL",
"KICH", "KIPAN", "KIRC", "KIRP", "LGG", "LIHC", "LUAD", "LUSC",
"STAD", "STES", "TGCT", "THCA", "THYM", "UCEC", "UCS", "UVM"),
gene A = c(2.53523182291, 4.24028537986,
4.2961196377, 5.704706725705, 3.872673336325, 4.237031758135,
4.158417821, 6.031765535715, 5.310256918635, 4.885279662985,
3.74332062144, 6.33283859333, 6.07383185768, 5.22031447524,
5.34321592399, 4.5604234962, 3.2689938787, 3.03710103601,
5.94956061183, 6.19829180068, 4.31473277382, 4.18386758335,
4.668459860855, 5.08274090402, 3.07739683262, 4.00955320565,
3.933397760305, 4.22861092745, 5.26711626188, 5.28281785129,
4.50236485242, 5.60167869065, 6.67313176408, 3.311560724255,
1.95099089988, 3.53933318793), gene B = c(1.74549550948,
4.283760946765, 4.16740610241, 5.5645134556, 5.73067480081,
4.658244464035, 4.57945171425, 8.89577605866, 4.83403271751,
2.930135381415, 1.62832568781, 5.31851912397, 2.119853482145,
4.86034209697, 5.52799299981, 4.287668059045, 1.21801953053,
4.04097131218, 5.77614874252, 5.440736309, 5.93769984273,
4.51994441418, 5.01470489422, 2.51045562166, 3.91270734164,
4.30825164659, 4.30399502979, 4.61294809206, 5.69423389893,
5.43082049652, 6.74529471152, 4.43835939502, 8.31310826563,
5.257437091785, 4.23880214229, 1.84655825028)), row.names = c(NA,
-36L), class = "data.frame")

R rna-seq • 1.1k views
1
Entering edit mode

What do you exactly mean by combined expression?

0
Entering edit mode

I'm honestly not sure. A reviewer asked I could add the combined expression of the two genes of interest. This is their exact wording "Add a table of the median RSEM normalized expression per cohort of gene A and gene B sorted by descending combined expression"

1
Entering edit mode

There is not enough context to understand what the reviewers are asking. Perhaps someone else may chime in with something useful.

1
Entering edit mode

This boils down to one's interpretation, as indeed the meaning is not clear. If the review process is interactive, you can simply ask the reviewer directly. If this is in a journal that doesn't have an interactive review system, I would write to the editor and ask them for more detailed instructions from the reviewer. I think that is better than doing something the reviewer didn't ask for.

1
Entering edit mode

They must mean something like this:

          GENE A   GENE B  Combined
DLBC          10       40        50
BRCA          20       20        40
LIHC          30        5        35
... ...
GBM            1        0         1