Dear Heidi, other users.
I have an SDS formatted file to import using
raw <- readCtData(files=c("SDS2.txt"), path=path, SDS=TRUE)
Error in `[.data.frame`(sample, , Ct) : undefined columns selected

This is done naively without setting arguments, which may well solve things.
I will try it. However, the SDS file seems to have 3 parts to it. 1) The
header, which is skipped when using SDS=TRUE, 2) the raw data in tab
delimited (the plate ID is missing and as there are multiple plates, I am
thinking I should add that in) and 3) There is a summary section at the end,
quite long.

Does readCtData understand the third summary data section? Or are the SDS
files I have slightly strange?

Also to extract raw data with Perl, I assume I need;

1) well number
2) plate id
3) sample
4) detector
5) task
6) CT

Is this enough information to carry out all tests with HTqPCR?

Thank you.

1) header section

SDS 2.2.2RQ Results 1.0
Filename Card A 1-10.sdm
Assay Type RQ Study
EmbeddedFile Card A (1) BX005 BX010 BX012 BX013 A
Run DateTime Fri May 22 11:53:04 BST 2009
Operator
ThermalCycleParams
EmbeddedFile Card A (2) BX007 BX008 BX011 Ref A
Run DateTime Wed Jul 22 14:38:58 BST 2009
Operator
.......etc, then 2) raw tab delim data

Well PlateID Sample Detector Task Ct delta Rn delta Ct Ct Avg Ct SD Avg
Delta Ct delta Ct SD Endo Ct Avg Endo Ct SD delta delta Ct RQ RQ Min
RQ Max Baseline
Type Baseline Start Baseline Stop Threshold Type Threshold Instrument Well
Status Rejected Filename
1 BX005 CSF3-Hs00236884_m1 Target Undetermined 0.12634672 40.0 20.051275
19.948725 Manual 3 15 Manual 0.60596806 201488 Card A (1) BX005 BX010 BX012
BX013 A
2 BX005 CSF2-Hs00171266_m1 Target 35.817932 3.3153937 35.817932 15.869207
19.948725 0.0 1.0 Manual 3 15 Manual 0.7333056 201488 Card A (1) BX005 BX010
BX012 BX013 A

..........etc, then finally 3) summary data.

Summary Data for Study Card A 1-10.sdm
Endogenous Control 18S-Hs99999901_s1
Calibrator BX005
Multiplicity Non-Multiplex
PlateID Sample Detector Avg delta Ct delta Ct SD delta delta Ct RQ RQ Min RQ
Max Threshold Sample Status
BX005 18S-Hs99999901_s1 0.59327465
BX010 18S-Hs99999901_s1 0.59327465
BX012 18S-Hs99999901_s1 0.59327465
BX013 18S-Hs99999901_s1 0.59327465

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