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Question: mas5 normalisation giving negetive value after using exprs()
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gravatar for kritikamish99
5 months 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 5 months ago by James W. MacDonald46k • written 5 months ago by kritikamish9910
1
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald46k 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 5 months ago by James W. MacDonald46k
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