[BioC] HTqPCR setCategories problem

[Michael Muratet]

Greetings

I have encountered a small problem when using the setCategories method:

s2010004660.cat <- setCategory(s2010004660, quantile=0.9,  
groups=sampleNames(s2010004660))
Categories after Ct.max and Ct.min filtering:
              wt_4wks mt_4wks wt_17wks mt_17wks
OK               582     571      566      578
Undetermined     186     197      202      190
Categories after standard deviation filtering:
              wt_4wks mt_4wks wt_17wks mt_17wks
OK               581     569      565      577
Undetermined     186     197      202      190
There were 50 or more warnings (use warnings() to see the first 50)
 > warnings()
Warning messages:
1: In `[<-.factor`(`*tmp*`, index, value = "Unreliable") :
   invalid factor level, NAs generated
2: In `[<-.factor`(`*tmp*`, index, value = "Unreliable") :
   invalid factor level, NAs generated
3: In `[<-.factor`(`*tmp*`, index, value = "Unreliable") :
   invalid factor level, NAs generated

other 47 warnings are the same

The categories that you get in the SDS data are "OK" and  
"Undetermined" and it seems to be unwilling to add the new level  
"Unreliable".  I tried to manually add the levels:

featureCategory(s2010004660)$wt_4wks <-  
factor(featureCategory(s2010004660)$wt_4wks,  
levels=c(levels(featureCategory(s2010004660)$wt_4wks),"Unreliable"))
featureCategory(s2010004660)$mt_4wks <-  
factor(featureCategory(s2010004660)$mt_4wks,  
levels=c(levels(featureCategory(s2010004660)$mt_4wks),"Unreliable"))
featureCategory(s2010004660)$wt_17wks <-  
factor(featureCategory(s2010004660)$wt_17wks,  
levels=c(levels(featureCategory(s2010004660)$wt_17wks),"Unreliable"))
featureCategory(s2010004660)$mt_17wks <-  
factor(featureCategory(s2010004660)$mt_17wks,  
levels=c(levels(featureCategory(s2010004660)$mt_17wks),"Unreliable"))

and get another error

Error in count[names(tab), i] <- tab : subscript out of bounds

Is this a bug or operator error?

Thanks

Mike

 > sessionInfo()
R version 2.11.0 (2010-04-22)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] HTqPCR_1.2.0       limma_3.4.0        RColorBrewer_1.0-2  
Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affy_1.26.0           affyio_1.16.0         gdata_2.7.1            
gplots_2.7.4          gtools_2.6.1          preprocessCore_1.10.0
[7] tools_2.11.0

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806