[BioC] siggenes failure
Louisa A Rispoli/AS/EXP/UTIA
larispoli at mail.ag.utk.edu
Wed Aug 6 17:36:07 CEST 2008
To all-
I have finally figured out how to use ebam and incorparate a database so I
can know what genes are interesting, or at least it was working yesterday
but no longer. For some reason the ebam is not the right S4 object though I
am using the same code as I did yesterday. I can not figure out where the
issue is, hopefully someone else's keen eyes can spot where it has gone
wrong.
Sincerely Louisa
YESTERDAYS Code
> library(siggenes)
Loading required package: multtest
> Filter.mas <- exprs(Cum.mas.filter)
> find.out <- find.a0(Filter.mas, cl, B=5000, rand=123456)
We're doing 12870 complete permutations
and randomly select 5000 of them.
> ebam.out <- ebam(find.out)
> ebam2excel(ebam.out, delta=0.9,file="Cumulus.csv", n.digits=4,
what="both", quote=FALSE)
Output is stored in Cumulus.csv
> genenames <- list.siggenes(ebam.out, 0.9)
> save.image("C:\\Documents and Settings\\Louisa Rispoli\\My
Documents\\Louisa\\Rebecca Payton\\HS Microarray\\Cumulus
Data\\Cumulus.Rdata")
> library(bovine.db)
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
> library(annaffy)
Loading required package: GO.db
Loading required package: KEGG.db
> aaf.handler()
[1] "Probe" "Symbol" "Description"
"Chromosome" "Chromosome Location"
[6] "GenBank" "Gene" "Cytoband"
"UniGene" "PubMed"
[11] "Gene Ontology" "Pathway"
> anncols <- aaf.handler()[c(1:3, 6:7,11:12)]
> anncols
[1] "Probe" "Symbol" "Description" "GenBank" "Gene"
"Gene Ontology" "Pathway"
> anntable <- aafTableAnn(genenames, "bovine.db", anncols)
> saveHTML(anntable, "Cumulus5000.html", title="Cumulus Data with 5000
permutations")
> sessionInfo()
R version 2.7.1 (2008-06-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tcltk splines tools stats graphics grDevices utils
datasets methods base
other attached packages:
[1] siggenes_1.14.0 multtest_1.20.0 affycoretools_1.12.1
annaffy_1.12.1 KEGG.db_2.2.0 biomaRt_1.14.0
[7] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0
RBGL_1.16.0 annotate_1.18.0 xtable_1.5-2
[13] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9
DBI_0.2-4 graph_1.18.1 limma_2.14.5
[19] bovinecdf_2.2.0 tkWidgets_1.18.0 DynDoc_1.18.0
widgetTools_1.16.0 simpleaffy_2.16.0 gcrma_2.12.1
[25] matchprobes_1.12.0 genefilter_1.20.0 survival_2.34-1
affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1
[31] Biobase_2.0.1
loaded via a namespace (and not attached):
[1] cluster_1.11.11 XML_1.94-0.1
TODAY'S CODE
> library(siggenes)
Loading required package: multtest
> Filter.mas <- exprs(Cum.mas.filter)
> find.out <- find.a0(Filter.mas, cl, B=5000, rand=123456)
We're doing 12870 complete permutations
and randomly select 5000 of them.
> ebamCum <- ebam(find.out)
> ebamCum
EBAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances
Fudge Factor: a0 = 0.0941
Delta Number FDR
1 0.9 77 0.0619
> CumNames <- list.siggenes(ebamCum, 0.9)
Error in list.siggenes(ebamCum, 0.9) :
no slot of name "row.sig.genes" for this object of class "table"
In addition: Warning message:
In list.siggenes(ebamCum, 0.9) :
trying to get slot "row.sig.genes" from an object (class "table") that is
not an S4 object
> summary(ebamCum, 0.9)
EBAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances
Delta: 0.9
a0: 0.0941
p0: 1
Cutlow: -2.7031
Cutup: 2.4761
Identified Genes: 77
Estimated FDR: 0.06191
Identified Genes (posterior >= 0.9):
Row z.value posterior local.fdr Name
1 6191 -4.160 0.9906 0.009395 Bt.26365.1.A1_at
2 5431 4.012 0.9909 0.009117 Bt.24179.1.A1_at
3 9987 3.917 0.9894 0.010574 Bt.8479.1.A1_at
4 8305 -3.857 0.9845 0.015473 Bt.4714.1.S1_at
5 6083 -3.714 0.9804 0.019568 Bt.2577.1.S1_at
6 4100 -3.567 0.9751 0.024895 Bt.21220.1.S1_at
7 3314 3.563 0.9816 0.018380 Bt.19889.1.A1_at
8 3986 3.523 0.9804 0.019572 Bt.20994.1.S1_at
9 7822 3.497 0.9796 0.020381 Bt.3797.1.S1_at
10 9166 -3.387 0.9666 0.033366 Bt.6438.1.A1_at
11 1573 -3.381 0.9663 0.033686 Bt.13993.2.S1_at
12 3759 3.366 0.9750 0.024994 Bt.20520.1.S1_at
13 1572 -3.289 0.9609 0.039091 Bt.13993.1.A1_at
14 7051 3.274 0.9712 0.028841 Bt.28332.1.S1_at
15 9507 3.265 0.9708 0.029246 Bt.7190.1.S1_at
16 4671 -3.264 0.9593 0.040720 Bt.2230.1.S2_at
> ebam2excel(ebamCum, delta=0.9,file="Cumulus.csv", n.digits=4,
what="both", quote=FALSE)
Length Class Mode
1 EBAM S4
R version 2.7.1 (2008-06-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tcltk splines tools stats graphics grDevices utils
datasets methods base
other attached packages:
[1] siggenes_1.14.0 multtest_1.20.0 affycoretools_1.12.1
annaffy_1.12.1 KEGG.db_2.2.0 biomaRt_1.14.0
[7] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0
RBGL_1.16.0 annotate_1.18.0 xtable_1.5-2
[13] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9
DBI_0.2-4 graph_1.18.1 limma_2.14.5
[19] bovinecdf_2.2.0 tkWidgets_1.18.0 DynDoc_1.18.0
widgetTools_1.16.0 simpleaffy_2.16.0 gcrma_2.12.1
[25] matchprobes_1.12.0 genefilter_1.20.0 survival_2.34-1
affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1
[31] Biobase_2.0.1
loaded via a namespace (and not attached):
[1] cluster_1.11.11 XML_1.94-0.1
"If we knew what we were doing, it wouldn't be called Research." - Albert
Einstein
Louisa Rispoli, Ph.D. Reproductive Physiology
Department of Animal Science
University of Tennessee, Knoxville
A105 Johnson Animal Research and Teaching Unit
1750 Alcoa Highway
Knoxville, TN 37920
phone:(865) 946-1874
fax:(865) 946-1010
email: lrispoli at utk.edu
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