[BioC] structure of cfx file for HTqPCR

[Brian Gorsuch [guest]]

Dear Sir/Madam,
I would like to submit a question and in doing so am very grateful for your time, effort and expertise in doing so.  I am just in the instruction phases of qPCR and using the Biorad iCylcer with cfx manager on a Dell optimplex 980, intel core i5, using R 2.15.0, with Windows XP prof 2002.  The cfx files when exported into excel format look nothing like the example given from within the HTqPCR example file.  The cfx exports both Ct and expression files, and includes all samples per page per plate.  When trying to call in HTqPCR after exporting as tab delim file I get error code:
 " error in data.frame(sample = 1:length(samples), row.names = samples) :
  row names supplied are of the wrong length
I have included HTqPCR sample file.txt, and original cfx ouput file.

18s is housekeeping, v656, v655 are KI adn WT.

I realize most of my problem must be in my not comprehending what the top row in the HTqPCR file stands for (X,  X.1, X2X3X4, etc)

Questions:
1. How should I structure the cfx files once exported to excel.
2. I assume from HTqPCR manual  that only one sample per file, so 10 files total (5 control mice vs 6 genes tested, 5 Ki mice with 6 genes tested).
3. Does a separate file need to be created for expression results?

I understand many of you are incredibly busy and I am extremely grateful for and respect your time and effort.  I apologize for what may seem simplistic questions.  I have taken R classes but seems all the software my lab is using including microarray is not what was used when some of these program were built, and my inexperience.

Sincerely,
Brian Gorsuch 


 -- output of sessionInfo(): 

HTqPCR program data file example:

 X1 Treatment A1  Passed Sample01 Gene1 Endogenous.Control X11.566983  X      X.1        X.2 X.3 X.4       X.5      X.6 FALSE.
1  2 Treatment A2  Passed Sample01 Gene2             Target    34.9502 NA 23.11739 0.10150807   0   1 0.7232906 1.382570  FALSE
2  3 Treatment A3  Passed Sample01 Gene3             Target  27.962915 NA 16.17094 0.09178536   0   1 0.7460847 

My file for error:
My cfx manager output file (Ct data only not expression file):

Well 	Fluor 	Content 	Target 	Sample 	Threshold Cycle ( C(t) ) 	C(t) Mean 	C(t) Std. Dev
A01 	SYBR 	Unkn-01 	18s 	v655 	13.44 	13.48 	0.056
A02 	SYBR 	Unkn-04 	18s 	v656 	14.22 	14.22 	0.000

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