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I am trying module preservation with WGCNA using my own data. I am plotting the summary statistics including Zsummary, medianRank, observed IGP and IGP permutation p-value for two comparison data sets.

When plotting the scatterplots for IGP & p-value vs. module size I get following error code. I have re-run code and done practice data with no problems but unsure how to correct for this error? Does anyone have any experience with this and know how to resolve? Thank you kindly

 plotData[[2]][, 3] = cr[[ref]][[test]]$Acutal.IGP
  plotData[[2]],[, 4] = -log(cr[[ref]][[test]]$p.value + 1e -4)

errror in plotData[[2]][, 3] = cr[[ref]][[test]]$Acutal.IGP
number of items to replace is not a multiple of replacement length`````

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My first guess is that there is a typo in your code, and Acutal.IGP should be Actual.IGP. I checked my tutorials and the word Acutal is in none of them, so I would assume you mistyped the variable name.

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  • $\begingroup$ Oh my gosh! I am so sorry, I have re-read this so many times! and re-typed. I apologise I will get another pair of eyes to check as well as me before posting again. Thank you so much! $\endgroup$ – Ruth Johnson Nov 11 '19 at 14:47

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