Hi Kipper,

Thanks so much, that worked perfectly!

Norm

From: Kipper Fletez-Brant [mailto:cafletezbrant@gmail.com]
Sent: Tuesday, February 25, 2014 12:05 PM
To: Norm Allaire
Cc: bioconductor@r-project.org
Subject: Re: [BioC] creating a qPCRset from Fluidigm 96*96 arrays in HTqPCR

Hi Norm,

Try re-running your code as follows:

temp <- readCtData(exFiles, path = exPath, n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip=12, sep=",")

You didn't have an '=' between skip and 12, so R didn't know how to process your input.

Best,
Kipper Fletez-Brant

On Tue, Feb 25, 2014 at 11:58 AM, Norm Allaire <norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com>> wrote:
Hi,

I'm new to R. I'm trying to analyze 8 Fluidgm 96 *96 plates (96 assays and 192 samples replicated 4 times). I downloaded and installed HTqPCR and I'm now trying to read in the raw data. I am using the "HTqPCR -high-throughput qPCR analysis in R and Bioconductor" April 14, 2011 as a guide but the example in section 13 is for 48*48 arrays. I tried to modify the 48*48 example to make it work with my files but it doesn't seem to work, I get the following error:

> temp <- readCtData(exFiles, path = exPath, n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip 12, sep=",")
Error: unexpected numeric constant in "temp <- readCtData(exFiles, path = exPath, n.features = 96 * 96, flag = 9, feature =5, type = 6, Ct =7, position= 1, skip 12"

Any thoughts or suggestions would be greatly appreciated!


Norm Allaire
Scientist II
Genetics and Genomics
Biogen Idec
14 Cambridge Center
Cambridge, MA 02142
Office:  617-679-2932
e-mail:  norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com><mailto:norm.allaire@biogenidec.com<mailto:norm.allaire@biogenidec.com>>

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