[Robast-commits] r372 - branches/robast-0.7/pkg/RobLoxBioC/man

[noreply at r-forge.r-project.org]

Author: stamats
Date: 2009-09-05 11:11:22 +0200 (Sat, 05 Sep 2009)
New Revision: 372

Modified:
   branches/robast-0.7/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd
   branches/robast-0.7/pkg/RobLoxBioC/man/robloxbioc.Rd
Log:
html-Links should work now in package RobLoxBioC

Modified: branches/robast-0.7/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd
===================================================================
--- branches/robast-0.7/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd	2009-09-05 08:47:00 UTC (rev 371)
+++ branches/robast-0.7/pkg/RobLoxBioC/man/KolmogorovMinDist.Rd	2009-09-05 09:11:22 UTC (rev 372)
@@ -27,7 +27,7 @@
   \item{mad0}{ scale estimate used if computed MAD is equal to zero. 
     Median and MAD are used as start parameter for optimization. }
   \item{bg.correct}{ if \code{TRUE} MAS 5.0 background correction is performed;
-    confer \code{\link[affy]{bg.correct.mas}}. }
+    confer \code{\link[affy:bgc]{bg.correct.mas}}. }
   \item{pmcorrect}{ if \code{TRUE} \code{log2(PM/MM)} is used. 
     If \code{FALSE} only \code{log2(PM)} is used. }
   \item{verbose}{ logical: if \code{TRUE}, some messages are printed. }

Modified: branches/robast-0.7/pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- branches/robast-0.7/pkg/RobLoxBioC/man/robloxbioc.Rd	2009-09-05 08:47:00 UTC (rev 371)
+++ branches/robast-0.7/pkg/RobLoxBioC/man/robloxbioc.Rd	2009-09-05 09:11:22 UTC (rev 372)
@@ -39,9 +39,9 @@
   \item{fsCor}{ logical: perform finite-sample correction. See function \code{\link[RobLox]{finiteSampleCorrection}}. }
   \item{mad0}{ scale estimate used if computed MAD is equal to zero}
   \item{bg.correct}{ if \code{TRUE} MAS 5.0 background correction is performed;
-    confer \code{\link[affy]{bg.correct.mas}}. }
+    confer \code{\link[affy:bgc]{bg.correct.mas}}. }
   \item{pmcorrect}{ method used for PM correction; \code{TRUE} calls an algorithm which is 
-    comparable to the algorithm of MAS 5.0; confer \code{\link[affy]{pmcorrect.mas}}. 
+    comparable to the algorithm of MAS 5.0; confer \code{\link[affy:pmcorrect]{pmcorrect.mas}}. 
     If \code{FALSE} only the PM intensities are used. }
   \item{normalize}{ logical: if \code{TRUE}, Affymetrix scale normalization is performed. }
   \item{add.constant}{ constant added to the MAS 5.0 expression values before the normalization
@@ -126,8 +126,8 @@
 %\note{}
 \seealso{\code{\link[RobLox]{roblox}}, \code{\link[RobLox]{rowRoblox}},
          \code{\link[affy]{AffyBatch-class}}, 
-         \code{\link[affy]{generateExprVal.method.mas}},
-         \code{\link[Biobase]{ExpressionSet-class}},
+         \code{\link[affy:generateExprVal.method.avgdiff]{generateExprVal.method.mas}},
+         \code{\link[Biobase:class.ExpressionSet]{ExpressionSet-class}},
          \code{\link[beadarray]{createBeadSummaryData}} }
 \examples{
 ## similar to rowRoblox of package RobLox