Hi Jenny,

These precious codes are really working fine for me!!!!!
Also, I went though all of the analysis I knew of the new ExpressionSet and
got no problem and more reasonable results even there are still have some
blank gene symbols.  One more question is I still have to build my own data
frame for annotation inforamtion summerization, in this case, I just follow
the online BioC manual,  but I got the error messege (see below).


Codes:
### add annotation info.
library("annotate")
library("yeast2.db")
annotation(esetsub) <- "yeast2.db"
# esetsub is a matrix with 5900 rows after removeProbes and filtration

probeIDs <- ls(yeast2GENENAME)     # Creates vector of all Affy IDs for this
chip.
symbols <- as.vector(unlist(mget(probeIDs,yeast2GENENAME)))   # Retrieves
gene descriptions
orf <- as.vector(unlist(mget(probeIDs,yeast2ORF)))      # Retrieves ORF

# build data frame
df <- as.data.frame(exprs(esetsub))
Annot <- data.frame(probeIDs, symbols, orf, df, row.names=NULL)
------------Error in data.frame(probeIDs, symbols, orf, df, row.names =
NULL) :
            arguments imply differing number of rows: 10928, 5900


Should I use the same vector as "maskedprobes" to subset the list??
Thank you in advance!!!!!!

Best regards,
Hui-Yi


On Thu, Oct 2, 2008 at 1:10 PM, Jenny Drnevich <drnevich@illinois.edu>wrote:

> 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]]
>>
>> _______________________________________________
>> Bioconductor mailing list
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
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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@illinois.edu
>

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