I am working on affymetrix cel files of zebrafish, and I have 74 normal and treated samples. For this I would like to perform wgcna analysis, but I don't know how to create trait file for this analysis. Can any solve My problem
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written
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rajasekargutha •
The simplest trait file just contains booleans for treated or non-treated, with 0 untreated an 1 treated
sample1 0
sample2 1
sample3 0
But it's far more valuable if you have more (quantitative) measurements, e.g. stress response, life time,... I have no idea what's available in your experimental set-up. I would recommend following the great tutorials on the WGCNA website: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/
Can you explain little further. What is life time means? How to take it as trait? Here samples are treated with metals and chemicals
Have you followed the tutorials? There are even youtube tutorials explaining in depth how to use WGCNA.
i followed the tutorial and watched youtube videos. but i am getting error in r code when i followed tutorial. especially at datTraits = allTraits[traitRows, -1] rownames(datTraits) = allTraits[traitRows, 1]
table(rownames(datTraits)==rownames(datExprFemale))
this code
And what is the error?
i am runnig wgcna r code by following ucla lab wgcna tutorial. i am finding a problem in trait file match to expression set...when i run a code like this i am ending with this error...can any one sort my problem traitData =read.csv("ClinicalTraits.csv") dim(traitData) names(traitData) allTraits=traitData[,c(2,3)] names(allTraits) Mice=rownames(datExprFemale) traitRows = match(Mice, allTraits$Mice) datTraits = allTraits[traitRows, -1]
traitRows [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 16 17 18 19 20 21 22 23 24 25 [26] 26 27 28 NA 30 31 32 33 34 35 36 37 38 39 40 41 42 43 NA NA NA 47 NA 49 50 [51] NA NA NA NA 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 [76] 76 77
why i am getting NA
Mice stress
1 GSM1088000_Robison-102-031009.CEL 1 2 GSM1088001_Robison-124-031009.CEL 1 3 GSM1088002_Robison-133-031009.CEL 0 4 GSM1088003_Robison-120-031009.CEL 0 5 GSM1088004_Robison-122-031009.CEL 0 6 GSM1088005_Robison-129-031009.CEL 0
this is my trait file
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