[BioC] readCtData() in HTqPCR with matrix of multiple samples

[Heidi Dvinge]

Hi Andrew,

> Hi I was wondering if you can read a tab delimited file of micro array
> data using readCtData() in HTqPCR as follows:
>
> Detector   SampleA   SampleB etc.
> Gene1      20             23
> Gene 2     32             25
> etc.
>
if multiple samples are present within a file, then readCtData expects
them to be arranged sequentially rather than side by side, since this is
the default output from the SDS analysis software.

However, if you simply have your data in a tabular format, you can create
your qPCRset object manually like this:

# Reading in all values
temp	<- read.delim('PCM_cardA-all-raw.txt')

# Making pesudo-data, just to illustrate the example
temp	<- matrix(sample(12:40, size=27*381, replace=TRUE), ncol=27)
rownames(temp)	<- paste("gene", 1:381)
colnames(temp)	<- paste("sample", 1:27)

# Make qPCRset object
q.raw	<- new("qPCRset",
	exprs=temp,
	featureNames=rownames(temp),
	sampleNames=colnames(temp),
	flag=as.data.frame(array("Passed", dim=dim(temp))),
	featureCategory=as.data.frame(array("OK", dim=dim(temp))))

If this doesn't work with your data for some reason, then please let me know.

HTH
\Heidi

> I've tried
>
> foo <- readCtData('file.txt', header=T,  n.features=381,
> samples=samples, n.data=27)
> # in this case there are 381 rows of Detectors and 27 samples
>
> But get the following error message:
>
>> foo <- readCtData('PCM_cardA-all-raw.txt', header=T,  n.features=381,
>> samples=samples, n.data=27)
> Error in `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined") :
>   only logical matrix subscripts are allowed in replacement
> In addition: Warning messages:
> 1: In readCtData("PCM_cardA-all-raw.txt", header = T, n.features = 381,  :
>   381 gene names (rows) expected, got 381
> 2: In matrix(sample[, Ct], ncol = n.data[i]) :
>   data length [381] is not a sub-multiple or multiple of the number of
> rows [15]
>
> Thanks,
> Andrew
>
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] HTqPCR_1.5.4       limma_3.6.9        RColorBrewer_1.0-2
> Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] affy_1.28.0           affyio_1.18.0         gdata_2.8.1
> [4] gplots_2.8.0          gtools_2.6.2          preprocessCore_1.12.0
> [7] tools_2.12.2
>