In HTqPCR, the header in SDS files is identified as the first line beginning with a hash mark (#). Newer SDS file formats use the word "Well" at the beginning of the header line instead. For that reason, HTqPCR fails to read recent SDS files. This can be solved easily by adding "Well" as one alternative when searching for the header in the SDS file. Also, newer SDS files have different column orders and multiple flag columns. Therefore, the default column indeces for SDS files should probably better be adjusted to the current SDS format and no flag column should be specified by default.

diff --git a/R/readCtData.R b/R/readCtData.R
index ce9a964..28f11f4 100644
--- a/R/readCtData.R
+++ b/R/readCtData.R
@@ -41,7 +41,7 @@ function(files,
     if (missing(column.info)) {
         column.info <- switch(format,
             plain    = list(flag=4, feature=6, type=7, position=3, Ct=8),
-            SDS    = list(flag=4, feature=6, type=7, position=3, Ct=8),
+            SDS    = list(feature=3, type=5, position=1, Ct=6),
             LightCycler    = list(feature="Name", position="Pos", Ct="Cp"),
             CFX    = list(feature="Content", position="Well", Ct="Cq.Mean"),
             OpenArray    = list(flag="ThroughHole.Outlier", feature="Assay.Assay.ID", type="Assay.Assay.Type", position="ThroughHole.Address", Ct="ThroughHole.Ct"),
@@ -172,7 +172,7 @@ function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...)
{
     # Scan through beginning of file, max 100 lines
     file.header <- readLines(con=readfile, n=100)
-    n.header <- grep("^#", file.header)
+    n.header <- grep("^(#|Well)", file.header)
     if (length(n.header)==0)
         n.header <- 0
     # Read data, skip the required lines

Hi Henrik, thanks for pointing this out, I wasn't aware that the SDS format had changed. I'll add this to the next release of the package.