[BioC] difference between rmaPLM and default fitPLM?

[Jenny Drnevich]

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