[BioC] Reading in data with HTqPCR

[Heidi Dvinge]

On 28 May 2010, at 16:01, deepak roshan wrote:

> 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...
>
You haven't actually read in any data in the example you provide  
below. data(qPCRraw) will load the qPCRset object called qPCRraw,  
which is an example dataset that comes with the HTqPCR package.  head 
(read.delim(file.path(path, "files.txt"))) is simply included to show  
you what's in the "files.txt" file - note that you only /display/ the  
content, you don't actually assign it to anything in R as you would  
do with "<-", using e.g.:
 > file.info <- read.delim(file.path(path, "files.txt"))
See the help pages ?head and ?read.delim if you're not sure about  
what the functions actually do.

In order to read in your own data, you need the function readCtData  
(and the parameter n.data). Examples of how to use the function are  
provided in ?readCtData and the HTqPCR vignette.

HTH
\Heidi

> 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