Hi,

I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe gene
expression value before further analysis. Earlier I was using filtration
function to filter out the lowest signals which I assumed from S. pombe.
However, this method seems not perfect since I got the result. Thus, I
turned to use altcdfenv package to create a S.C. only env. But I got some
errors when I applied this env for next analysis. I really appreciate your
help!!!

Here is the code:
## data importing
library("affy")
library("limma")
targets <- readTargets("fed_total.txt")
raw.data <- ReadAffy(filenames = targets $ filename)

## create altcdfenv
library(altcdfenvs)
getCdfEnvAffy(raw.data); library(yeast2cdf)

twocdf <- wrapCdfEnvAffy(yeast2cdf, 496, 496, "yeast2cdf"); print(twocdf)

sc.ids <- scan("sc_IDs.txt", what="")        ###  got  5749 s.c. ids
sc.only.cdf <- twocdf[sc.ids]
sc.only.cdf @ envName <- "S_cerevisiae_IDs Only"; print(sc.only.cdf)

### apply this subset-cdf to "affybatch"
env.sc.cdf <- as(sc.only.cdf, "environment")
raw.data @cdfName <- "sc.only.cdf"
save(raw.data, sc.only.cdf, env.sc.cdf, file="sc_only_cdf.rda")

###  start further analysis
eset <- rma(aaa)

----- got errors:
Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) :
  invalid object for 'as.environment'

###  tried pa calls--- also got errors
eset.pm <- mas5calls(raw.data)

Getting probe level data...
Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) :
  invalid object for 'as.environment'
Error in as.matrix(pm(object)) :
  error in evaluating the argument 'x' in selecting a method for function
'as.matrix'


If there is any mistake in my codes????
Any suggestions are appreciated!

Many thanks!
Hui-Yi



> sessionInfo()
R version 2.7.2 (2008-08-25)
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] altcdfenvs_2.2.0     hypergraph_1.12.0    Biostrings_2.8.18
 [4] makecdfenv_1.18.0    scatterplot3d_0.3-27 yeast2.db_2.2.0
 [7] affycoretools_1.12.1 annaffy_1.12.1       KEGG.db_2.2.0
[10] gcrma_2.12.1         matchprobes_1.12.1   biomaRt_1.14.1
[13] RCurl_0.9-3          GOstats_2.6.0        Category_2.6.0
[16] RBGL_1.16.0          annotate_1.18.0      xtable_1.5-3
[19] GO.db_2.2.0          AnnotationDbi_1.2.2  RSQLite_0.7-0
[22] DBI_0.2-4            graph_1.18.1         gplots_2.6.0
[25] gdata_2.4.2          gtools_2.5.0         Heatplus_1.10.0
[28] RColorBrewer_1.0-2   genefilter_1.20.0    survival_2.34-1
[31] yeast2cdf_2.2.0      limma_2.14.6         affy_1.18.2
[34] preprocessCore_1.2.1 affyio_1.8.1         Biobase_2.0.1

loaded via a namespace (and not attached):
[1] cluster_1.11.11 XML_1.94-0.1

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