Question: To get expression data from GEO
0
gravatar for Jerry Cholo
5.6 years ago by
Jerry Cholo190
Jerry Cholo190 wrote:
Hello, I would like to have expression data for GSE27597. When I ran following command line: data1 = getGEO("GSE27597") I noticed that there are two files related to this GSE (see below): Found 2 file(s) GSE27597-GPL13243_series_matrix.txt.gz Using locally cached version: C:\Users\AppData\Local\Temp\RtmpodgO6C/GSE27597-GPL13243_series_matrix .txt.gz Using locally cached version of GPL13243 found here: C:\Users\AppData\Local\Temp\RtmpodgO6C/GPL13243.soft GSE27597-GPL5175_series_matrix.txt.gz Using locally cached version: C:\Users\AppData\Local\Temp\RtmpodgO6C/GSE27597-GPL5175_series_matrix. txt.gz Using locally cached version of GPL5175 found here: C:\Users\AppData\Local\Temp\RtmpodgO6C/GPL5175.soft When I ran following line datExpr = exprs (data1) to get expression data I did not get the main data that includes more samples, but I got the smaller dataset that has few samples. May someone let me know how I could deal with this problem? Thanks, Jerry [[alternative HTML version deleted]]
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ADD COMMENTlink modified 5.6 years ago by Vegard Nygaard110 • written 5.6 years ago by Jerry Cholo190
Answer: To get expression data from GEO
0
gravatar for Vegard Nygaard
5.6 years ago by
Norway
Vegard Nygaard110 wrote:
Hi Jerry. The GSE27597 data set seems to consist of data from two different array platforms, so getGEO returns a list of two ExpressionSet objects. You need to use the list accessor, [[]], to get the individual elements. Something like this: library(GEOquery) data1 = getGEO("GSE27597") datExpr1 = exprs (data1[[1]]) dim(datExpr1) # the first smaller data set datExpr2 = exprs (data1[[2]]) dim(datExpr2) # the second larger And your line datExpr = exprs (data1) Just gave an error for me, so You might be using an old version of GEOquery. This is my sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.28.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 XML_3.95-0.2 Vegard. On 2014-03-25 23:47, Jerry Cholo wrote: > Hello, > > > I would like to have expression data for GSE27597. When I ran > following > command line: > > > > data1 = getGEO("GSE27597") > > > > I noticed that there are two files related to this GSE (see below): > > > > > > Found 2 file(s) > > > GSE27597-GPL13243_series_matrix.txt.gz > > Using locally cached version: > C:\Users\AppData\Local\Temp\RtmpodgO6C/GSE27597-GPL13243_series_matr ix.txt.gz > > Using locally cached version of GPL13243 found here: > > C:\Users\AppData\Local\Temp\RtmpodgO6C/GPL13243.soft > > > > GSE27597-GPL5175_series_matrix.txt.gz > > Using locally cached version: > C:\Users\AppData\Local\Temp\RtmpodgO6C/GSE27597-GPL5175_series_matri x.txt.gz > > Using locally cached version of GPL5175 found here: > > C:\Users\AppData\Local\Temp\RtmpodgO6C/GPL5175.soft > > > > When I ran following line > > > > datExpr = exprs (data1) > > > > to get expression data I did not get the main data that includes more > samples, but I got the smaller dataset that has few samples. > > > > May someone let me know how I could deal with this problem? > > > > Thanks, > > Jerry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.6 years ago by Vegard Nygaard110
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