Hi All,

I am trying to use samr to characterize differential expression in a time course. 3 reps of 4 timepoints, affymetrix arabidopsis ATH1 chips. I'm using "One class timecourse". Using chips I generated at the beginning of the year I have experienced no problems, but in expression sets containing data from newer experiments produce the following error message (regardless of preprocessing by MAS5 or gcrma):

>samr.data=list(x=exprs(COLcilscM5),y=COLcilscM5$time,geneid=featureNames(COLcilscM5),genenames=featureNames(COLcilscM5),logged2=FALSE)
>samr.obj=samr(samr.data,resp.type="One class timecourse",time.summary="slope")
123456789101112Error in quantile.default(sd, seq(0, 1, len = 101)) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE

>samr.data=list(x=exprs(COLcilscGC),y=COLcilscGC$time,geneid=featureNames(COLcilscGC),genenames=featureNames(COLcilscGC),logged2=TRUE)

>samr.obj=samr(samr.data,resp.type="One class timecourse",time.summary="slope")

123456789101112Error in quantile.default(sd, seq(0, 1, len = 101)) : 

  missing values and NaN's not allowed if 'na.rm' is FALSE
The pData for these expression sets is organized:
> pData(COLcilscM5)
             sample        time
bot1330w.CEL      1 1Time1Start
bot1332w.CEL      2      1Time2
bot1334w.CEL      3      1Time3
bot1336w.CEL      4   1Time4End
bot1516.CEL       5 1Time1Start
bot1517.CEL       6 1Time1Start
bot1518.CEL       7      1Time2
bot1519.CEL       8      1Time2
bot1520.CEL       9      1Time3
bot1521.CEL      10      1Time3
bot1522.CEL      11   1Time4End
bot1523.CEL      12   1Time4End

The newer expression sets do contain an additional element name "se.exprs" in addition to the "exprs" and "phenoData" in the older ones. However, removing this element does not help. No missing values or NaN's could be found in the expression sets using variations on length(which(is.na(exprs(COLcilscM5)))) etc. Changing 'na.rm' to TRUE doesn't help.

Help/Suggestions gratefully received.
Thanks
Steven
 



      
	[[alternative HTML version deleted]]

