wgcna trait file for affymetrix cel files

Question

[rajasekargutha]

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

Answer 1

[WouterDeCoster]

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/

[rajasekargutha]

Can you explain little further. What is life time means? How to take it as trait? Here samples are treated with metals and chemicals

[WouterDeCoster]

Have you followed the tutorials? There are even youtube tutorials explaining in depth how to use WGCNA.

[rajasekargutha]

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]

show that row names agree

table(rownames(datTraits)==rownames(datExprFemale))

this code

[WouterDeCoster]

And what is the error?

[rajasekargutha]

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

[rajasekargutha]

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