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Question: GEOquery
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gravatar for Julie Zhu
7.6 years ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k 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') Found 1 file(s) GSE6547_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE6547/GSE6547_seri es_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"
ADD COMMENTlink modified 7.6 years ago by Sean Davis21k • written 7.6 years ago by Julie Zhu3.8k
0
gravatar for Julie Zhu
7.6 years ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:
With sessionInfo() this time. Thanks! Julie On 3/31/10 6:07 PM, "Julie Zhu" <julie.zhu at="" 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') > Found 1 file(s) > GSE6547_series_matrix.txt.gz > trying URL > 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE6547/GSE6547_se ries_matri > x.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" Here is the sessionInfo > 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] GEOquery_2.11.3 RCurl_1.3-1 [3] bitops_1.0-4.1 ChIPpeakAnno_1.2.13 [5] limma_3.2.3 org.Hs.eg.db_2.3.6 [7] GO.db_2.3.5 RSQLite_0.8-2 [9] DBI_0.2-5 AnnotationDbi_1.8.2 [11] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.14.2 [13] Biostrings_2.14.12 IRanges_1.4.16 [15] multtest_2.2.0 Biobase_2.6.1 [17] biomaRt_2.2.0 loaded via a namespace (and not attached): [1] MASS_7.3-4 splines_2.10.1 survival_2.35-7 tools_2.10.1 XML_2.6-0 ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://www.umassmed.edu/pgfe/faculty/zhu.cfm
ADD COMMENTlink written 7.6 years ago by Julie Zhu3.8k
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gravatar for Sean Davis
7.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Wed, Mar 31, 2010 at 6:07 PM, Zhu, Julie <julie.zhu at="" 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_se ries_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" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 7.6 years ago by Sean Davis21k
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_se ries_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" > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > 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 [[alternative HTML version deleted]]
ADD REPLYlink written 7.6 years ago by Julie Zhu3.8k
On Thu, Apr 1, 2010 at 9:51 AM, Zhu, Julie <julie.zhu at="" umassmed.edu=""> wrote: > 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! The data are downloaded from GEO. No numerical processing is applied. GEO simply stores the data as supplied by the submitter and GEOquery just parses these data into bioconductor objects. There are no .CEL files involved at all. > 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! You would need to start with the supplemental files: getGEOSuppFiles("GSE6547") This will create a directory in your working directory called "GSE6547". Into that directory, all the available supplemental files for that GSE record will be downloaded. In this case, there happens to be a .tar file with .CEL files in it. You can use those .CEL files in the usual way and take the phenoData from a call to getGEO() to add annotation. Hope that helps. Sean > Best regards, > > Julie > > > On 3/31/10 6:38 PM, "Sean Davis" <seandavi at="" gmail.com=""> wrote: > > On Wed, Mar 31, 2010 at 6:07 PM, Zhu, Julie <julie.zhu at="" 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_s eries_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" >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > >> 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 > >
ADD REPLYlink written 7.6 years ago by Sean Davis21k
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