Dear all,


I am analyzing data obtained using the HuGene2.0-st arrays from affymetrix.

I have used aroma for preprocessing and limma for diff. expression
analysis. After multiple testing I lost significance and therefore I want
to filter out genes that do not have a potential to be significantly
different.

So I have created an expression set after rma


plm <- RmaPlm(csN)

fit(plm, verbose=verbose)

ces <- getChipEffectSet(plm)

eset <- extractExpressionSet(ces)

ans <- nsFilter(eset)

I am getting an error at this point:

Error in if (nchar(annChip) == 0) stop("'eset' must have a valid annotation
slot") :
  argument is of length zero

.

I understand that is because the annotation field is empty. But how can I
overcome this?

Thanks Andreia

the ces object

ChipEffectSet:
Name: Jurkat_0_vs_over_2
Tags: RBC,QN,RMA
Path:
Documents/analysis_affy_arrays/plmData/Jurkat_0_vs_over_2,RBC,QN,RMA/HuGene-2_0-st
Platform: Affymetrix
Chip type: HuGene-2_0-st,r3_binary,monocell
Number of arrays: 6
Names: Ju_0_1_1, Ju_0_2_2, Ju_0_3_3, ..., Ju_34c_5_6 [6]
Time period: 2013-03-27 16:56:07 -- 2013-03-27 16:56:08
Total file size: 3.08MB
RAM: 0.01MB
Parameters: {}

the eset object:

ExpressionSet (storageMode: lockedEnvironment)
assayData: 53617 features, 6 samples
  element names: exprs
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:


sessionInfo()

R version 2.15.3 (2013-03-01)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
 [1] hgu95av2.db_2.8.0      org.Hs.eg.db_2.8.0     RSQLite_0.11.2
DBI_0.2-5              AnnotationDbi_1.20.7   BiocInstaller_1.8.3
genefilter_1.40.0
 [8] GenomeGraphs_1.18.0    biomaRt_2.14.0         limma_3.14.4
gplots_2.11.0          MASS_7.3-23            KernSmooth_2.23-10
caTools_1.14
[15] gdata_2.12.0           gtools_2.7.1           Biobase_2.18.0
BiocGenerics_0.4.0     aroma.affymetrix_2.8.0 affxparser_1.30.2
aroma.apd_0.2.3
[22] R.huge_0.4.1           aroma.light_1.28.0     aroma.core_2.8.3
matrixStats_0.6.2      R.rsp_0.8.2            R.devices_2.1.3
R.cache_0.6.5
[29] R.filesets_2.0.0       R.utils_1.23.2         R.oo_1.13.0
affy_1.36.1            R.methodsS3_1.4.2

loaded via a namespace (and not attached):
 [1] IRanges_1.16.6        PSCBS_0.30.0          RCurl_1.95-4.1
XML_3.96-1.1          affyio_1.26.0         annotate_1.36.0
bitops_1.0-4.2
 [8] digest_0.6.3          parallel_2.15.3       preprocessCore_1.20.0
splines_2.15.3        stats4_2.15.3         survival_2.37-4
tools_2.15.3
[15] xtable_1.7-1          zlibbioc_1.4.0





---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

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