I have a set of rt-pcr data to analyse. However, the SDS files I have in hads do not contain Ct information: rather, they contain raw fluorescence values for all 40 cycles. So far, the RT-PCR packages I have found have been unable to load these (ddCt, HTqPCR).

Are there any R packages that would:
A) Read such files
B) Provide functions for automatically selecting a Ct threshold from the raw fluorescence information?

Alternatively, if no such files exist, can anyone point out any kind of file format specification explaining the meanings of the various columns?

Here is an excerpt from one of the files:

SDS 2.4	RQ Results	1.0
Filename	Immunoscore_PCa_1
PlateID	
Assay Type	Relative Quantification
Run DateTime	2/19/15 4:04:41 PM
Operator	
ThermalCycleParams	

Sample Information
																		
Well	Sample Name	Detector	Task	Reporter	Rn	1	2	[…]	39	40	FOS	HMD	LME	EW	BPR	NAW	HNS	HRN
11	1133-PN-07	18S-Hs99999901_s1	ENDO	FAM		1.6612182	1.6526943	[…]	7.7634277	7.6926284								
6	1133-PN-07	CCL1-Hs00171072_m1	TARG	FAM		1.888895	1.9043217	[…]	2.0366857	2.049185						true		
31	1133-PN-07	CCL24-Hs00171082_m1	TARG	FAM		1.3389541	1.3350073	[…]	3.384823	3.5847595								
30	1133-PN-07	CCR6-Hs01890706_s1	TARG	FAM		2.4079435	2.4371755	[…]	7.772515	8.113571								
[…]																		
NAP	LPL