[BioC] questions about altcdfenv

[lgautier at altern.org]

> 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).



For removing particular whole probe sets, I would defend that the
ease-of-use of "altcdfenvs" is at least as easy (as shown in the vignette
"ngenomeschips").

Removing probes within existing probe sets currently requires few lines of
code, but I still have the hope to find the time to write either functions
or documentation on how to do so in the future.



L.


> 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
>
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