Question: error in vsn package
0
gravatar for Angel
4.0 years ago by
Angel40
Berlin
Angel40 wrote:

hi,

i was going to normalize my microarray datasets by vsn package but i got this error

what does this mean please?

 a <- vsn(mycounts)
Note: 
The function 'vsn' has been superseded by 'vsn2'.
The function 'vsn' remains in the package for backward compatibility,
but for new projects, please use 'vsn2'.
 
Error in getIntensityMatrix(intensities, verbose) : 
  'intensities' was found to be a data.frame, but contains non-numeric columns.
> a <- vsn2(mycounts)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘vsn2’ for signature ‘"data.frame"’

ADD COMMENTlink modified 4.0 years ago by Wolfgang Huber13k • written 4.0 years ago by Angel40
Answer: error in vsn package
0
gravatar for Wolfgang Huber
4.0 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

You need to call vsn2 on an object that has one of the supported classes.

> showMethods("vsn2")
Function: vsn2 (package vsn)
x="AffyBatch"
x="ExpressionSet"
x="matrix"
x="NChannelSet"
x="numeric"
x="RGList"

Please have a look at the vignette of the vsn package and at the manual page of the vsn2 function, this will save you a lot of time. There is also a paper that explains the method:

Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002;18 Suppl 1:S96-104. Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M.

Wolfgang

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Wolfgang Huber13k

sorry Dear Wolfgang,

i have 8 CEL files and i am going to perform variance stabilization on them. then i did like below

> setwd("E:/Affy data")

> library(affy)

> library(vsn)

> celFiles <- list.celfiles()
> affyraw=ReadAffy(filenames = celFiles)
> affyraw.vsn2=vsn2(affyraw)
vsn2: 506944 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit.

but hereafter  i could not figure out what to do by reading the vsn manual...may you help me please?

thank you

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Angel40

You probably want to do

eset <- justvsn(celFiles)

and then proceed with your analysis.

ADD REPLYlink written 4.0 years ago by James W. MacDonald51k
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