[BioC] HTqPCR - how to read data file with multiple samples
heidi at ebi.ac.uk
Fri Jan 8 09:40:20 CET 2010
originally HTqPCR only read in 1 sample per file. I've recently added the
parameter n.data to readCtData() to indicate the number of sample in each
file being processed (along with fixing a few bugs). I still need to
submit this to BioC though, so you can either wait a few days and get this
from the the devel repository, or if it's urgent I can send you the
corrected readCtData() function off-list.
> I have a data file (created by SDS), with 6 samples, like this:
> # Status Sample Detector Task Avg Ct
> 1 Analyzed 1 MammU6-4395470 Endogenous Control 22.733
> 2 Analyzed 2 MammU6-4395470 Endogenous Control 22.582
> 3 Analyzed 3 MammU6-4395470 Endogenous Control 22.656
> 4 Analyzed 4 MammU6-4395470 Endogenous Control 22.785
> 5 Analyzed 5 MammU6-4395470 Endogenous Control 22.684
> 6 Analyzed 7 MammU6-4395470 Endogenous Control 22.411
> I tried running:
> readCtData("Data.txt", SDS=TRUE, n.features=381, type=5, Ct=6,
> header=TRUE, feature=4)
> the HTqPCR package reads the data file as if there were only 1 sample:
> An object of class "qPCRset"
> Size: 381 features, 1 samples
> Feature types: Endogenous Control, Target
> Feature names: MammU6-4395470 MammU6-4395470 MammU6-4395470 ...
> Feature classes:
> Feature categories: OK
> Sample names: Data NA NA ...
> How do I read the data into HTqPCR so that it recognizes that I have 6
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives:
More information about the Bioconductor