Dear list users,

 

I am running ReadAffy() function under 

 

R version 2.10.0 (2009-10-26) 

i386-pc-mingw32 

 

locale:

[1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255   

[3] LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C                  

[5] LC_TIME=Hebrew_Israel.1255    

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods  

[7] base     

 

other attached packages:

[1] RColorBrewer_1.0-2 Heatplus_1.16.0    limma_3.2.1       

[4] affy_1.24.2        Biobase_2.6.1     

 

loaded via a namespace (and not attached):

[1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.0        

> 

 

>From some reason the following code works

 

C.anno = read.delim(file="gal/Citrus.gal",stringsAsFactors=FALSE)

targets = read.delim(file="targets/Targets.txt",stringsAsFactors=FALSE)

 

C.raw =  ReadAffy(filenames = targets$FileName,

                  celfile.path = "data",

                  sampleNames =
paste(targets$Target,targets$Repeat,sep="")

  )

 

C.raw@phenoData = new("AnnotatedDataFrame",data = targets)

C.raw@featureData = new("AnnotatedDataFrame",data = C.anno)

 

whereas this one

 

C.raw =  ReadAffy(filenames = targets$FileName,

                  celfile.path = "data",

                  sampleNames =
paste(targets$Target,targets$Repeat,sep=""),

                  phenoData = new("AnnotatedDataFrame",data = targets),

                  featureData = new("AnnotatedDataFrame",data =C.anno)

  )

 

 

does not.

 

I get the following error message:

 

Error: the following are not valid files:

    data/new("AnnotatedDataFrame", data = C.anno)

In addition: Warning message:

In AllButCelsForReadAffy(..., filenames = filenames, widget = widget,  :

  sampleNames not same length as filenames. Using filenames as
sampleNames instead

 

 

!! Targets and C.anno are data.frames, since they were read by
read.delim() function.

 

Can you think of why is that?

 

 

Thanks, 

Ron

 

 


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