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Question: mas5 normalisation giving negetive value after using exprs()
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gravatar for kritikamish99
11 days ago by
India
kritikamish9910 wrote:

Hi all

I used Mas5 normalisation over my cel file. After normalisation i have done exprs() call

I am getting negetive value for this

I have not any fold change or log FC over this data

 

Code :-

setwd("MCF7/data")
cels = list.files("MCF7/data", pattern = ".CEL")
raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="hgu133a2cdf")

mas.norm=mas5(raw.data)#mas5
mas.exprs=exprs(mas.norm)

mas.exprs is having negetive value

Can any one suggest me how is this possible

Also how can i import mas.norm file for reading norm data

ADD COMMENTlink modified 11 days ago by James W. MacDonald45k • written 11 days ago by kritikamish9910
1
gravatar for James W. MacDonald
11 days ago by
United States
James W. MacDonald45k wrote:

There is no guarantee that you won't have negative values from the MAS5.0 algorithm. It's simply a robust average of the PM - MM probe intensities, scaled to (in the case of the defaults) a value of 500. That's usually a large enough value to scale to, in order to eliminate negative values, but there's nothing in the code to preclude any negative values.

ADD COMMENTlink written 11 days ago by James W. MacDonald45k
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