[BioC] Error in calculating P-values with Genefilter function

[Brad Cattrysse [guest]]

To whom it may concern,

I am having trouble with the genefilter function in R. I am attempting to extract genes from 7 arrays using a p-value of 0.01 using the following code:

Func7P0.01<-filterfun(Anova(class7,p=0.01))
Func7P0.01
Anova7_P0.01<-genefilter(SCDexprs7,Func7P0.01)
Anova7_P0.01

Creating Func7P0.01 works fine, but when I run the genefilter using my data matrix and Func7P0.01 i get the following error.


> Anova7_P0.01<-genefilter(SCDexprs7,Func7P0.01)
Error in if (fstat < p) return(TRUE) : 
  missing value where TRUE/FALSE needed


and when I runtraceback(), I get: 

> traceback()
4: fun(x)
3: FUN(newX[, i], ...)
2: apply(expr, 1, flist)
1: genefilter(SCDexprs7, Func7P0.01)


Im not entirely sure what is going on, but when I extract genes from the same 7 arrays, plus another array (8 arrays total) using the same code structure (below) it works fine.


Func8P0.01<-filterfun(Anova(class8,p=0.01))
Func8P0.01
Anova8_P0.01<-genefilter(SCDexprs8,Func8P0.01)
Anova8_P0.01


Any help with this matter would be greatly appreciated as I am not sure what else to try.

Thanks in advance!
Brad Cattrysse


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

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

other attached packages:
 [1] pd.mogene.1.1.st.v1_3.8.0 RSQLite_0.11.3           
 [3] DBI_0.2-6                 ggplot2_0.9.3.1          
 [5] e1071_1.6-1               class_7.3-7              
 [7] pvac_1.8.0                pgmm_1.0                 
 [9] mclust_4.1                cluster_1.14.4           
[11] genefilter_1.42.0         oligoData_1.8.0          
[13] oligo_1.24.0              Biobase_2.20.0           
[15] oligoClasses_1.22.0       BiocGenerics_0.6.0       

loaded via a namespace (and not attached):
 [1] affxparser_1.32.0     affy_1.38.1           affyio_1.28.0        
 [4] annotate_1.38.0       AnnotationDbi_1.22.5  BiocInstaller_1.10.1 
 [7] Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8      
[10] colorspace_1.2-2      dichromat_2.0-0       digest_0.6.3         
[13] ff_2.2-11             foreach_1.4.0         GenomicRanges_1.12.2 
[16] grid_3.0.0            gtable_0.1.2          IRanges_1.18.0       
[19] iterators_1.0.6       labeling_0.1          MASS_7.3-26          
[22] munsell_0.4           plyr_1.8              preprocessCore_1.22.0
[25] proto_0.3-10          RColorBrewer_1.0-5    reshape2_1.2.2       
[28] scales_0.2.3          splines_3.0.0         stats4_3.0.0         
[31] stringr_0.6.2         survival_2.37-4       tools_3.0.0          
[34] XML_3.95-0.2          xtable_1.7-1          zlibbioc_1.6.0       
> 

--
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