Dear All,

I am trying to single channel analysis for my data and i get "In
remlscore(y, X, Z) : reml: Max iterations exceeded" this error. I did not
get this error before and i was trying to reanalyze this data and encounter
this error. I also updated Statmod package but still get this error. I
appreciate any help in this regard.

Here are the commands list :

targets<-readTargets("targets.txt")
>
RG<-read.maimages(targets,source="genepix",wt.fun=wtflags(weight=0),columns=list(R="F635
Median",G="F532 Median",Rb="B635",Gb="B532"))
Read 13961538.gpr
Read 13961556.gpr
Read 13961428-2.gpr
Read 13961652.gpr
Read 13961645.gpr
Read 13961646.gpr
Read 13961649.gpr
Read 13961635.gpr
Read 13961661.gpr
Read 13961800.gpr
> RG$genes<-readGAL()
> spottypes<-readSpotTypes("Spottypes.txt")
> RG <- backgroundCorrect(RG, method="normexp", offset=50)
Green channel
Corrected array 1
Corrected array 2
Corrected array 3
Corrected array 4
Corrected array 5
Corrected array 6
Corrected array 7
Corrected array 8
Corrected array 9
Corrected array 10
Red channel
Corrected array 1
Corrected array 2
Corrected array 3
Corrected array 4
Corrected array 5
Corrected array 6
Corrected array 7
Corrected array 8
Corrected array 9
Corrected array 10
> MA <- normalizeWithinArrays(RG)
> MA.Aq<-normalizeBetweenArrays(MA,method="Aquantile")
>
> targets2<-targetsA2C(targets)
> targets2
     channel.col SlideNumber       FileName Identity Target
1.1            1    13961538   13961538.gpr   RAO103   RT30
1.2            2    13961538   13961538.gpr   RAO103    RT0
2.1            1    13961556   13961556.gpr    RAO61   RT30
2.2            2    13961556   13961556.gpr    RAO61    RT0
3.1            1    13961428 13961428-2.gpr    RAO40   RT30
3.2            2    13961428 13961428-2.gpr    RAO40    RT0
4.1            1    13961652   13961652.gpr   RAO123    RT0
4.2            2    13961652   13961652.gpr   RAO123   RT30
5.1            1    13961645   13961645.gpr   RAO306    RT0
5.2            2    13961645   13961645.gpr   RAO306   RT30
6.1            1    13961646   13961646.gpr   RAO312    RT0
6.2            2    13961646   13961646.gpr   RAO312   RT30
7.1            1    13961649   13961649.gpr    Con32   CT30
7.2            2    13961649   13961649.gpr    Con32    CT0
8.1            1    13961635   13961635.gpr    Con53   CT30
8.2            2    13961635   13961635.gpr    Con53    CT0
9.1            1    13961661   13961661.gpr    Con87    CT0
9.2            2    13961661   13961661.gpr    Con87   CT30
10.1           1    13961800   13961800.gpr   Con106    CT0
10.2           2    13961800   13961800.gpr   Con106   CT30
> u<-unique(targets2$Target)
> f<-factor(targets2$Target,levels=u)
> design<-model.matrix(~0+f)
> colnames(design)<-u
>  corfit<-intraspotCorrelation(MA.Aq,design)
Loading required package: statmod
Warning messages:
1: In remlscore(y, X, Z) : reml: Max iterations exceeded
2: In remlscore(y, X, Z) : reml: Max iterations exceeded

Thanks
Priyanka

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