I'm trying to parse the probe set ids from the file 'GSE15543' ,the GDS file name of the same study is GDS4027.
There is a problem while parsing the probe ids from GSE.
GSE file:
eset2 <- getGEO('GSE15543')[[1]]
fData(eset2)[nrow(fData(eset)),] #nrow = 54675
Output:
ID GB_ACC SPOT_ID Species Scientific Name Annotation Date Sequence Type
NA.41561 <NA> <NA> <NA> <NA> <NA> <NA>
Sequence Source Target Description Representative Public ID Gene Title
NA.41561 <NA> <NA> <NA> <NA>
Gene Symbol ENTREZ_GENE_ID RefSeq Transcript ID Gene Ontology Biological Process
NA.41561 <NA> <NA> <NA> <NA>
Gene Ontology Cellular Component Gene Ontology Molecular Function
NA.41561
GDS file:
gds <- getGEO('GDS4027')
eset = GDS2eSet(gds)
fData(eset)[nrow(fData(eset)),] #nrow = 54675
Output:
ID Gene title Gene symbol Gene ID UniGene title
AFFX-TrpnX-M_at AFFX-TrpnX-M_at
UniGene symbol UniGene ID Nucleotide Title GI GenBank Accession
AFFX-TrpnX-M_at NA
Platform_CLONEID Platform_ORF Platform_SPOTID Chromosome location
AFFX-TrpnX-M_at --Control
Chromosome annotation GO:Function GO:Process GO:Component GO:Function ID
AFFX-TrpnX-M_at
GO:Process ID GO:Component ID
AFFX-TrpnX-M_at
As displayed in the above outputs, I am not able to obtain the probe id while using the expression set created using gse file.
In short, the trouble is
> rownames(exprs(eset2))[1] [1] "1007_s_at" > rownames(exprs(eset2))[54675] [1] "NA.41561"
I'm not able to parse all the probe ids (e.g "NA.41561") and therefore not able to map these to gene symbols.
I would like to parse all the probe set ids from the gse file, map the probe ids to the gene symbols. Any help will be much appreciated.
I'm not sure what is going on. This is what I see:
> gse = getGEO('GSE15543')[[1]] Found 1 file(s) GSE15543_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE15nnn/GSE15543/matrix/GSE15543_series_matrix.txt.gz' Content type 'application/x-gzip' length 14491926 bytes (13.8 MB) ================================================== downloaded 13.8 MB Parsed with column specification: cols( .default = col_double(), ID_REF = col_character() ) See spec(...) for full column specifications. File stored at: /var/folders/hq/pzgtdx7j55j0g7r4647vqzrr2yvxz9/T//RtmpVfLEKO/GPL570.soft |============================================================================================================| 100% 80 MB > gse ExpressionSet (storageMode: lockedEnvironment) assayData: 54675 features, 33 samples element names: exprs protocolData: none phenoData sampleNames: GSM388740 GSM388741 ... GSM388772 (33 total) varLabels: title geo_accession ... cell type:ch1 (34 total) varMetadata: labelDescription featureData featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (54675 total) fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total) fvarMetadata: Column Description labelDescription experimentData: use 'experimentData(object)' Annotation: GPL570 > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib 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] bindrcpp_0.2.2 GEOquery_2.48.0 Biobase_2.40.0 ExperimentHub_1.6.0 AnnotationHub_2.12.0 [6] BiocGenerics_0.26.0 ... > fData(gse)[nrow(gse),] ID GB_ACC SPOT_ID Species Scientific Name Annotation Date Sequence Type AFFX-TrpnX-M_at AFFX-TrpnX-M_at --Control Homo sapiens Oct 6, 2014 Control sequence Sequence Source AFFX-TrpnX-M_at Affymetrix Proprietary Database Target Description AFFX-TrpnX-M_at B. subtilis /GEN=trpD, trpC /DB_XREF=gb:K01391.1 /NOTE=SIF corresponding to nucleotides 2880-3359 of gb:K01391.1, not 100% identical /DEF=B.subtilis tryptophan (trp) operon, complete cds. Representative Public ID Gene Title Gene Symbol ENTREZ_GENE_ID RefSeq Transcript ID AFFX-TrpnX-M_at AFFX-TrpnX-M Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function AFFX-TrpnX-M_atI'll look into the issue on Windows when I get a chance.
On Linux,
cannot open URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL570&form=text&view=full'sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] GEOquery_2.36.0 Biobase_2.30.0 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] RCurl_1.95-4.11 bitops_1.0-6 XML_3.98-1.16
Any suggestion on how to resolve this error?
Yes. Use a current version of R/Bioconductor. You are using a version that is almost 3 years old, which is no longer supported. As Sean has already shown, the current version works fine.