>
> Dear sir,
>
> thank you for your all help. iam facing some problems in raedCtData  
> step. i have 99 sample but it is deading only 6 samples.how the  
> sample numbers can be incereased to 99. details of the  session is  
> given below
>
> deepak
>
> > n.samples <- 99
> > readCtData(files = files$File, path = path, n.features = 48, flag  
> = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE,  
> SDS = FALSE, n.data = 1, samples, na.value = 40)
> An object of class "qPCRset"
> Size:  48 features, 6 samples
> Feature types:           Endogenous Control, Target
> Feature names:           CCNF-Hs00171049_m1 RBL2-Hs00180562_m1  
> CCND1-Hs00277039_m1 ...
> Feature classes:
> Feature categories:      OK
> Sample names:            Sample1 Sample2 Sample3 ...
> Warning message:
> In readCtData(files = files$File, path = path, n.features = 48,  :
>   Not enough sample names provided; using Sample1, Sample2, ...  
> instead
>
Hello Deepak,

there is nothing in readCtData specifying that only 6 samples can be  
read. Defining a variable n.samples isn't going to change that, since  
you don't actually use this variable anywhere. What matters here is  
if your length(files$File) is 99. What does just:

 > files$File

say?

In the example data there are only 6 files, but if I read some of  
them multiple times, I can say:

 > exPath <- system.file("exData", package="HTqPCR")
 > exFiles <- read.delim(file.path(exPath, "files.txt"))
 > raw <- readCtData(files=exFiles$File[c(1:6,2:5,1:6)], path=exPath)
 > raw
An object of class "qPCRset"
Size:  384 features, 16 samples
Feature types:		 Endogenous Control, Target
Feature names:		 Gene1 Gene2 Gene3 ...
Feature classes:	
Feature categories:	 OK, Undetermined
Sample names:		 sample1 sample2 sample3 ...

However, note that you do get a warning message about sample names.   
In your readCtData command, you include "samples". This is meant to  
be a character vector of sample names, if you don't want to use file  
names as sample names. Have you actually defined a variable called  
"samples" anywhere?? If you have your sample names in e.g. a vector  
called my.samplenames, then you need to run readCtData with:

readCtData(files = files$File, path = path, n.features = 48, flag =  
4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, SDS =  
FALSE, n.data = 1, samples=my.samplenames, na.value = 40)

If not, then skip the "samples" parameter altogether and say:

readCtData(files = files$File, path = path, n.features = 48, flag =  
4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, SDS =  
FALSE, n.data = 1, na.value = 40)

Does that change anything?
\Heidi



> > head(read.delim(file.path(path, "files.txt")))
>           File Treatment
> 1  Sample4.txt     Tumor
> 2 Sample67.txt     Tumor
> 3 Sample80.txt     Tumor
> 4 Sample44.txt     Tumor
> 5 Sample76.txt     Tumor
> 6 Sample94.txt    Normal
> > tail(read.delim(file.path(path, "files.txt")))
>            File Treatment
> 94 Sample37.txt     Tumor
> 95 Sample32.txt     Tumor
> 96 Sample33.txt     Tumor
> 97 Sample34.txt     Tumor
> 98 Sample25.txt     Tumor
> 99 Sample26.txt    Normal
>
> > sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United  
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           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           gplots_2.7.4          gtools_2.6.2           
> preprocessCore_1.10.0
> [7] tools_2.11.0
>
>


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