Problem facing for retrieving Phalanx_id from geo data set in R

Question

[fahim]

Hi

I am facing a lot of problem for retrieving Phalanx_id to gene symbol .My geo data i downloaded from geo dataset and stored in a excel file.Where the first column of my data set is ID_REF as bellow and rest of the column are the sample id lke GSM2527022

PH_hs_0000002
PH_hs_0000003
PH_hs_0000004
PH_hs_0000005
PH_hs_0000006
PH_hs_0000007
PH_hs_0000008
PH_hs_0000009
PH_hs_0000010
PH_hs_0000011
PH_hs_0000012
PH_hs_0000013
PH_hs_0000014
PH_hs_0000015
PH_hs_0000016
PH_hs_0000017
PH_hs_0000018

There is almost 31741 ID_REF. so how can i convert them into gene symbol?

[GenoMax]

Please do not post similar content in multiple threads. You have already received comments for this question in:

Problem for retrieving gene symbol from ID_REF

[fahim]

I gave the post again because i am still now unable to retrieve my gene symbol from that ID_REF by R

Answer 1

[GenoMax]

Did you look at the files that were linked? The NCBI GPL file link (was in last post, posted again) contains a mapping of ID's you have and Gene Names. You can download the table, read it into R and then select the two columns you need (ID and Gene_Symbol, excerpt below)

ID  Group   Entrez_gene REFSEQ  GB_ACC  RNA_nucleotide_gi   Protein_accession.version   Gene_symbol Description Chromosome  Map_location    Genomic_Specific    Orientation GO_id_function  GO_id_componen  GO_id_process   GO_term_function    GO_term_component   GO_term_process Ensembl_gene    Ensembl_transcript  Ensembl_protein Unigene_cluster Uniprot_id  SEQUENCE    SPOT_ID
PH_hs_0000002   1   1089    NM_001817.2 NM_001817.2 71143131    NP_001808.2 CEACAM4 carcinoembryonic antigen-related cell adhesion molecule 4   19  19q13.2 No  -       GO:0005624,GO:0005887,GO:0016020            membrane fraction,integral to plasma membrane,membrane      ENSG00000105352 ENST00000456892,ENST00000472081,ENST00000221954 ENSP00000403837,ENSP00000221954 Hs.12   O75871  AACTATTCAAGCCTATTATTGGCACAAGGGGAAAACGGCAGAAGGGAGCCCTCTCATTGC    
PH_hs_0000003   1   4049    NM_001159740.1  NM_001159740.1  229092380   NP_001153212.1  LTA lymphotoxin alpha (TNF superfamily, member 1)   6   6p21.3  No  +   GO:0005102,GO:0005125,GO:0005164,GO:0005515 GO:0005576,GO:0005615,GO:0016020    GO:0006917,GO:0006959,GO:0007165,GO:0007267,GO:0007584,GO:0032496,GO:0048147,GO:0048535 receptor binding,cytokine activity,tumor necrosis factor receptor binding,protein binding   extracellular region,extracellular space,membrane   induction of apoptosis,humoral immune response,signal transduction,cell-cell signaling,response to nutrient,response to lipopolysaccharide,negative regulation of fibroblast proliferation,lymph node development   ENSG00000226275,ENSG00000226979,ENSG00000238130,ENSG00000223919,ENSG00000173503,ENSG00000231408,ENSG00000230279 ENST00000473355,ENST00000412851,ENST00000464086,ENST00000426845,ENST00000464821,ENST00000441939,ENST00000487391,ENST00000432632,ENST00000490708,ENST00000383304,ENST00000476761,ENST00000383303,ENST00000461499,ENST00000454550,ENST00000479906,ENST00000436519,ENST00000468015,ENST00000448630,ENST00000466460,ENST00000456789,ENST00000471842,ENST00000418386,ENST00000489638,ENST00000454783,ENST00000498217,ENST00000383499,ENST00000481446,ENST00000400272 ENSP00000412555,ENSP00000402413,ENSP00000387924,ENSP00000416337,ENSP00000372793,ENSP00000372791,ENSP00000416509,ENSP00000395976,ENSP00000407133,ENSP00000395895,ENSP00000413450,ENSP00000403495,ENSP00000372991,ENSP00000383131 Hs.36   P01374,Q5STV3   GTGAGAGGGCATGCGCACAAGGCTGACCAAGAGAGAAAGAAGTAGGCATGAGGGATCACA    
PH_hs_0000004   1   38  NM_000019.3 NM_000019.3 223890189   NP_000010.1 ACAT1   acetyl-CoA acetyltransferase 1  11  11q22.3-q23.1   Yes +   GO:0003985,GO:0005515,GO:0008415,GO:0016740,GO:0046872  GO:0005739,GO:0005743,GO:0005759    GO:0008152  acetyl-CoA C-acetyltransferase activity,protein binding,acyltransferase activity,transferase activity,metal ion binding mitochondrion,mitochondrial inner membrane,mitochondrial matrix metabolic process   ENSG00000075239 ENST00000265838 ENSP00000265838 Hs.232375   P24752  CATGCTAATTCAGAAGCTGTAGACAACCTCTGCTATTTAAGGAGACAACCCTATGTGACC    

[fahim]

Yes i saw this but i want to retrieve this by R programming