[BioC] difference between rmaPLM and default fitPLM?
Jenny Drnevich
drnevich at illinois.edu
Wed Aug 13 23:16:32 CEST 2008
Hi again,
I've gone through the codes of fitPLM and rmaPLM, and I think the
difference between them is in the modelparam; rmaPLM instead uses
md.param, which has only two of the list items of modelparam (I don't
pretend to understand what they are). Each function also calls a
different .Call code, and the one rmaPLM uses outputs NaNs for all
the se.*.coefs. So, my questions remain:
1. Are rmaPLM and fitPLM with defaults supposed to return the same
expression values? If so, why aren't they, and if not, what is fitPLM
calculating?
2. Is there anyway to get the se.chip.coefs for RMA expression values?
Thanks!
Jenny
At 01:18 PM 8/13/2008, Jenny Drnevich wrote:
>HI,
>
>I'm getting a difference in the output of rmaPLM() and the default
>fitPLM(). I thought the default settings of fitPLM was supposed to
>be the RMA model, at least the vignette calls it a RMA-style PLM.
>Besides differences in the coefs/RMA values produced, rmaPLM is not
>outputting the se.chip.coefs slot, which is the standard error
>estimates for the chip coefficients that I want. See code and
>sessionInfo() below. I'm stepping through the code of each right now
>to figure out where the differences are, but I thought maybe someone
>could help me.
>
>Thanks,
>Jenny
>
> > raw <- ReadAffy()
>
> > raw
>AffyBatch object
>size of arrays=1002x1002 features (8 kb)
>cdf=Mouse430_2 (45101 affyids)
>number of samples=4
>number of genes=45101
>annotation=mouse4302
>notes=
>
> > rma.plm1 <- fitPLM(raw)
> > rma.plm2 <- rmaPLM(raw)
> > coefs(rma.plm1)[1:5,]
> ctrl ipi Dmp1 ipi+Dmp1
>1415670_at 11.02547 11.94682 11.07018 11.97461
>1415671_at 12.33057 11.79736 12.25891 11.85637
>1415672_at 11.38321 11.27387 11.36435 11.27967
>1415673_at 10.03639 10.30681 10.02795 10.50375
>1415674_a_at 10.45065 10.39834 10.53324 10.41134
> > coefs(rma.plm2)[1:5,]
> ctrl ipi Dmp1 ipi+Dmp1
>1415670_at 10.710135 11.64534 10.751418 11.64572
>1415671_at 12.414390 11.86388 12.337369 11.92163
>1415672_at 11.584338 11.46070 11.549982 11.51548
>1415673_at 9.902446 10.20577 9.933505 10.41233
>1415674_a_at 10.228274 10.13993 10.301835 10.18136
> > rma.rma <- rma(raw)
>Background correcting
>Normalizing
>Calculating Expression
> > exprs(rma.rma)[1:5,]
> ctrl ipi Dmp1 ipi+Dmp1
>1415670_at 10.710135 11.64534 10.751418 11.64572
>1415671_at 12.414390 11.86388 12.337369 11.92163
>1415672_at 11.584338 11.46070 11.549982 11.51548
>1415673_at 9.902446 10.20577 9.933505 10.41233
>1415674_a_at 10.228274 10.13993 10.301835 10.18136
> > se(rma.plm1)[1:5,]
> ctrl ipi Dmp1 ipi+Dmp1
>1415670_at 0.02452685 0.02395422 0.02431190 0.02582995
>1415671_at 0.02061485 0.02152285 0.02013362 0.02067196
>1415672_at 0.03053776 0.02985205 0.03011108 0.03238839
>1415673_at 0.04038712 0.03987544 0.04036288 0.03978057
>1415674_a_at 0.02810474 0.02876715 0.02745431 0.02860643
> > se(rma.plm2)[1:5,]
> ctrl ipi Dmp1 ipi+Dmp1
>1415670_at NaN NaN NaN NaN
>1415671_at NaN NaN NaN NaN
>1415672_at NaN NaN NaN NaN
>1415673_at NaN NaN NaN NaN
>1415674_a_at NaN NaN NaN NaN
> > 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] splines tools stats graphics grDevices utils datasets
>[8] methods base
>
>other attached packages:
> [1] mouse4302cdf_2.2.0 affyQCReport_1.18.0 geneplotter_1.18.0
> [4] lattice_0.17-8 RColorBrewer_1.0-2 simpleaffy_2.16.0
> [7] made4_1.14.0 ade4_1.4-9 affyPLM_1.16.0
>[10] affycoretools_1.12.0 annaffy_1.12.1 KEGG.db_2.2.0
>[13] gcrma_2.12.1 matchprobes_1.12.0 biomaRt_1.14.0
>[16] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0
>[19] genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0
>[22] annotate_1.18.0 xtable_1.5-2 GO.db_2.2.0
>[25] AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4
>[28] graph_1.18.1 limma_2.14.5 affy_1.18.2
>[31] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.1
>[34] RWinEdt_1.8-0
>
>loaded via a namespace (and not attached):
>[1] cluster_1.11.11 grid_2.7.1 KernSmooth_2.22-22 XML_1.94-0.1
>
>
>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at illinois.edu
>
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Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu
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