[BioC] siggenes sam2excel Error

[Holger Schwender]

Does the analysis work if you use

> sumis.names = read.table("sumis.names", header=TRUE, stringsAsFactors=FALSE)

If not, then I will have a look on this tomorrow.

Holger

-------- Original-Nachricht --------
> Datum: Wed, 6 Apr 2011 09:37:39 -0700 (PDT)
> Von: joseph <jdsandjd at yahoo.com>
> An: Holger Schwender <holger.schw at gmx.de>
> CC: bioconductor at r-project.org
> Betreff: Re: [BioC] siggenes sam2excel Error

> Hi Holger
> here is my code, I also attached the data files.
> 
> sumis.data = read.table("sumis.data", header = T)
> > sumis.data[1:3, ]
>   Y3 Y4 O1 O2 O3
> 1 37 47 43 35 15
> 2 40 40 28 23 17
> 
> sumis.names=read.table("sumis.names", header = T)
> sumis.names[1:3, ]
> [1] chr1_829531_830948_8  chr1_834144_836446_8  chr1_859152_861734_10
> 13110 Levels: chr1_100088009_100088618_8 chr1_10015120_10015990_8 
> chr1_100207922_100208694_8 chr1_100276024_100277063_8
> chr1_100370747_100371526_8 
> ... chrY_7201522_7203267_8
> 
> cl=c(rep(0,2), rep(1,3))
> 
> sam.out = sam(sumis.data, cl, rand = 123, gene.names = sumis.names)
> > summary(sam.out)
> SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances 
>   s0 = 37.2339  (The 100 % quantile of the s values.) 
>   Number of permutations: 10 (complete permutation) 
>  MEAN number of falsely called variables is computed.
>    Delta   p0  False Called    FDR cutlow cutup   j2    j1
> 1    0.1 0.18 1085.5   6562 0.0298 -0.682 0.650 6511 12969
> 2    0.2 0.18  690.2   6531 0.0190 -0.682 0.834 6511 13000
> 3    0.4 0.18  657.2   6511 0.0182 -0.682   Inf 6511 13020
> 4    0.5 0.18  657.2   6511 0.0182 -0.682   Inf 6511 13020
> 5    0.6 0.18  657.2   6511 0.0182 -0.682   Inf 6511 13020
> 6    0.7 0.18  617.7   6131 0.0181 -0.713   Inf 6131 13020
> 7    0.9 0.18  264.7   2643 0.0180 -1.056   Inf 2643 13020
> 8    1.0 0.18  123.4   1234 0.0180 -1.253   Inf 1234 13020
> 9    1.1 0.18   42.7    427 0.0180 -1.473   Inf  427 13020
> 10   1.2 0.18    0.4      4 0.0180 -2.066   Inf    4 13020
> 
> 
> > sam2excel(sam.out, 0.5, file="sumis.sam.csv", n.digits = 2, what =
> "both", 
> >entrez = FALSE, quote = FALSE)
> Error in if (all(rownames(mat.sig) != as.character(1:nrow(mat.sig))))
> mat.sig <- 
> data.frame(mat.sig,  : 
> 
>   missing value where TRUE/FALSE needed
> > 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ________________________________
> From: Holger Schwender <holger.schw at gmx.de>
> To: joseph <jdsandjd at yahoo.com>; bioconductor at r-project.org
> Sent: Wed, April 6, 2011 1:33:01 AM
> Subject: Re: [BioC] siggenes sam2excel Error
> 
> Hi Joseph,
> 
> I have just tested sam2excel against several situations which might cause
> this 
> error. But it works perfectly for me. So without seeing your R code and
> your 
> data, I actually have no idea why you get this error.
> 
> Best,
> Holger
> 
> 
> -------- Original-Nachricht --------
> > Datum: Tue, 5 Apr 2011 08:47:37 -0700 (PDT)
> > Von: joseph <jdsandjd at yahoo.com>
> > An: bioconductor at r-project.org
> > Betreff: [BioC] siggenes sam2excel Error
> 
> > Hi
> > I get an error when I use sam2excel to export sam output:
> > > sam2excel(sam.out, 0.1, file="sam.out.csv", n.digits = 2, what =
> "both",
> > quote 
> > >= FALSE, entrez = FALSE)
> > Error in if (all(rownames(mat.sig) != as.character(1:nrow(mat.sig))))
> > mat.sig <- 
> > data.frame(mat.sig,  : 
> > 
> >   missing value where TRUE/FALSE needed
> > 
> > The gene.names in my data are not annotated genes; they are genomic
> > locations 
> > (chr2_128148639_128149977,  chr2_128175315_128176406 …)
> >  Thank you for your help
> > Joseph
> > 
> > 
> > > sessionInfo()
> > R version 2.12.1 RC (2010-12-10 r53825)
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> > 
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> > 
> > attached base packages:
> > [1] splines   stats     graphics  grDevices utils     datasets  methods 
> > base    
> > 
> > 
> > other attached packages:
> > [1] siggenes_1.24.0 multtest_2.6.0  Biobase_2.10.0  sparcl_1.0.1  
> > 
> > loaded via a namespace (and not attached):
> > [1] cluster_1.13.2    compHclust_1.0-1  fastcluster_1.0.4
> flashClust_1.01 
> >  
> > MASS_7.3-9        survival_2.36-2   tools_2.12.1    
> > 
> > > 
> > 
> >     [[alternative HTML version deleted]]
> > 
> 
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