Question: wgcna trait file for affymetrix cel files
0
gravatar for rajasekargutha
3.1 years ago by
India
rajasekargutha20 wrote:

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

rna-seq • 1.1k views
ADD COMMENTlink modified 3.1 years ago by WouterDeCoster39k • written 3.1 years ago by rajasekargutha20
0
gravatar for WouterDeCoster
3.1 years ago by
Belgium
WouterDeCoster39k wrote:

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/

ADD COMMENTlink written 3.1 years ago by WouterDeCoster39k

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

ADD REPLYlink written 3.1 years ago by rajasekargutha20

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

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by WouterDeCoster39k

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

ADD REPLYlink written 3.1 years ago by rajasekargutha20

And what is the error?

ADD REPLYlink written 3.1 years ago by WouterDeCoster39k

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

ADD REPLYlink written 3.1 years ago by rajasekargutha20
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

ADD REPLYlink written 3.1 years ago by rajasekargutha20
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