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 â¦)
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]]
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]]
>
--
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@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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