Hi Sean,

Thanks for the quick response!

Looks like the expressionSet has been log2 transformed and summarized. Is it correct? Did you use rma method to summarize the probe level data? I am wondering whether expression value in expressionSet in gds[[1]] is also background corrected and normalized. If yes, what methods have been applied? Thanks!

With CEL files at hand, I usually do the following,

require(affy)
Data = ReadAffy(celfile.path="thepath")
eset<-rma(Data)
library("simpleaffy")
Data.qc <- qc(Data)
avbg(Data.qc)
percent.present(Data.qc)
......

I am wondering what would be the equivalent steps to apply to the expressionSet obtained from getGEO method? Thanks so much for your help!

Best regards,

Julie


On 3/31/10 6:38 PM, "Sean Davis" <seandavi@gmail.com> wrote:

On Wed, Mar 31, 2010 at 6:07 PM, Zhu, Julie <Julie.Zhu@umassmed.edu> wrote:
> Hi,
>
> First of all I would like to thank the developers for developing such a
> useful package!
>
> I downloaded a dataset using GEOquery package successfully as following.
> However, I could not convert it to eSet or get metadata out of it. Could you
> please let me know what I did wrong and how to proceed? Thanks so much for
> your help!
>
> Best regards,
>
> Julie
>
>  > gds <- getGEO('GSE6547')

Hi, Julie.  Thanks for the kind words.

gds is a list:

class(gds)
names(gds)

gds[[1]]

You asked for a GSE record with GSEMatrix=TRUE, so the default is to
return a list of ExpressionSets; see the help for getGEO().  The list
is due to some oddities of the GSE Matrix format that limits each GSE
Matrix file to 255 samples.

Hope that answers your question.

Sean

> Found 1 file(s)
> GSE6547_series_matrix.txt.gz
> trying URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE6547/GSE6547_series_mat
> rix.txt.gz'
> ftp data connection made, file length 1739964 bytes
> opened URL
> ==================================================
> downloaded 1.7 Mb
>
> File stored at:
> /tmp/RtmpaOAhXo/GPL200.soft
>
>>eset <- GDS2eSet(gds, do.log2 = TRUE)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "Meta", for signature
> "list"
>
>> Meta(gds)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "Meta", for signature
> "list"
>> Table(gds)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "Table", for signature
> "list"
>> Columns(gds)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "Columns", for signature
> "list"
>
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> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-apple-darwin8.11.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] GEOmetadb_1.6.0                     GEOquery_2.11.3
 [3] RCurl_1.3-1                         bitops_1.0-4.1
 [5] ChIPpeakAnno_1.2.13                 limma_3.2.3
 [7] org.Hs.eg.db_2.3.6                  GO.db_2.3.5
 [9] RSQLite_0.8-2                       DBI_0.2-5
[11] AnnotationDbi_1.8.2                 BSgenome.Ecoli.NCBI.20080805_1.3.16
[13] BSgenome_1.14.2                     Biostrings_2.14.12
[15] IRanges_1.4.16                      multtest_2.2.0
[17] Biobase_2.6.1                       biomaRt_2.2.0


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