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

Andrew Yee yee at post.harvard.edu
Sat Mar 19 20:32:20 CET 2011

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

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]


> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [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

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

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