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Steve Chatfield
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10
@steve-chatfield-3832
Last seen 9.6 years ago
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$time,geneid=featureNa
mes(COLcilscM5),genenames=featureNames(COLcilscM5),logged2=FALSE)
>samr.obj=samr(samr.data,resp.type="One class
timecourse",time.summary="slope")
123456789101112Error in quantile.default(sd, seq(0, 1, len = 101)) :
missing values and NaN's not allowed if 'na.rm' is FALSE
>samr.data=list(x=exprs(COLcilscGC),y=COLcilscGC$time,geneid=featureNa
mes(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
lengthwhichis.na(exprs(COLcilscM5)))) etc. Changing 'na.rm' to TRUE
doesn't help.
Help/Suggestions gratefully received.
Thanks
Steven
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