sir,

 I have 99 sample and they are tumor and normal but when i give command to
read the raw data it is reading only 6 sample and for > show(raw) the out
put is 6 samples. is this package is limited for 6 sample if we can change
the sample how it has to be done i tried using > n.sample <- 99 ot was not
working the detail of the session in here...

How to change feature class this not my class, how change the sample
numbers,change name of gene

> "n.samples <- 99"
[1] "n.samples <- 99"
> show(qPCRraw)
An object of class "qPCRset"
Size:  384 features, 6 samples
Feature types:           Endogenous Control, Target
Feature names:           Gene1 Gene2 Gene3 ...
Feature classes:         Kinase, Marker, TF
Feature categories:      OK, Undetermined
Sample names:            sample1 sample2 sample3 ...


>
> "n.samples <- 99"
[1] "n.samples <- 99"
> data(qPCRraw)
> data(qPCRpros)
> class(qPCRraw)
[1] "qPCRset"
attr(,"package")
[1] ".GlobalEnv"
> head(read.delim(file.path(path, "files.txt")))
       File Treatment
1 DC004.txt     Tumor
2  D289.txt     Tumor
3 N143A.txt     Tumor
4 N143C.txt    Normal
5  D330.txt     Tumor
6  D153.txt     Tumor
> 99.samples
Error: unexpected symbol in "99.samples"
> n.sample<-99.sample
Error: unexpected symbol in "n.sample<-99.sample"
> n.samples <- 99
> n.wells <- 48
> head(read.delim(file.path(path, "files.txt")))
       File Treatment
1 DC004.txt     Tumor
2  D289.txt     Tumor
3 N143A.txt     Tumor
4 N143C.txt    Normal
5  D330.txt     Tumor
6  D153.txt     Tumor
> data(qPCRraw)
> data(qPCRpros)
> class(qPCRraw)
[1] "qPCRset"
attr(,"package")
[1] ".GlobalEnv"
> show(qPCRraw)
An object of class "qPCRset"
Size:  384 features, 6 samples
Feature types:           Endogenous Control, Target
Feature names:           Gene1 Gene2 Gene3 ...
Feature classes:         Kinase, Marker, TF
Feature categories:      OK, Undetermined
Sample names:            sample1 sample2 sample3 ...
> sessionInfo()
R version 2.11.0 (2010-04-22)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] HTqPCR_1.2.0       limma_3.4.0        RColorBrewer_1.0-2
Biobase_2.8.0
loaded via a namespace (and not attached):
[1] affy_1.26.1           affyio_1.16.0         gdata_2.8.0
[4] gplots_2.7.4          gtools_2.6.2          preprocessCore_1.10.0
[7] tools_2.11.0
>
Thanking you




-- 
Deepak Roshan V G
Laboratory Of Cell Cycle Regulation  &   Molecular Oncology
Division of Cancer Research
Regional Cancer Centre
Thiruvananthapuram
Kerala, India 695 011

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