How to calculate combined expression of two genes
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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", 
                                  "COAD", "COADREAD", "DLBC", "ESCA", "GBM", "GBMLGG", "HNSC", 
                                  "KICH", "KIPAN", "KIRC", "KIRP", "LGG", "LIHC", "LUAD", "LUSC", 
                                  "MESO", "OV", "PAAD", "PCPG", "PRAD", "READ", "SARC", "SKCM", 
                                  "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
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1
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What do you exactly mean by combined expression?

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0
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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"

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1
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There is not enough context to understand what the reviewers are asking. Perhaps someone else may chime in with something useful.

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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.

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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
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