[BioC] questions about altcdfenv

[Jenny Drnevich]

Hi Hui-Yi,

See this recent post about another way to remove probe sets:

https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html

This will temporarily remove the probe sets from the regular 
yeast2cdf, and it's much easier to use than atlcdfenvs if you only 
want to remove particular probe sets or individual probes (it can't 
reorganize probes into other probe sets). It's also better than 
simply filtering out the S. pombe probe sets after an ExpressionSet 
is created, because those unwanted probe sets will still be used in 
whatever algorithm you used to make the ExpressionSet from the 
AffyBatch object. All you need is a list of the unwanted probe sets 
IDs. Let me know if you have any questions.

Cheers,
Jenny

At 01:56 PM 10/1/2008, Hui-Yi Chu wrote:
>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
>
>         [[alternative HTML version deleted]]
>
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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