i'm uploading an expression dataset of the format:
ILMN_1698554 7.95821798587323 7.94260716460775 ….
ILMN_2061446 7.85347403140808 7.91246250778809…..
and I would like to load the annotation data. If I select to automatically download the annotation using Illumina_Human it doesn't map. When I pull Illumina_Human from the ftp site the format is as follows:
Probe ID Clone Name Genbank Acc UniGene ID EntrezGene ID Gene Symbol & Name Gene Synonyms Human TC Human GC RefSeq Acc TC PubMed Ref GO TGI Annotation Phy Map Genetic Marker Mouse ortholog Rat ortholog Zebrafish ortholog Xenopus ortholog Cattle ortholog Elegans ortholog Yeast ortholog Dog ortholog Chicken ortholog
1-A-1 HG_010_00001 NM_005745 Hs.522817 10134 BCAP31; B-cell receptor-associated protein 31 DXS1357E 6C6-AG CDM BAP31
1-A-2 HG_010_00002 NM_014587 Hs.243678 30812 SOX8; SRY (sex determining region Y)-box 8 MGC24837
1-A-3 HG_010_00003 NM_014332 Hs.86492 23676 SMPX; small muscle protein, X-linked - THC2472864 GC20161 NM_014332 GO:0005634(nucleus) GO:0005737(cytoplasm) GO:0006941(striated muscle contraction) UP|Q5VSM2_HUMAN (Q5VSM2) Small muscle protein, X-linked, complete chrX (21,634,012-21,686,151) RH41821 TC1655538 TC580455 TC303647 TC279016 TC357955 TC47460 TC231741 TC246204
I don't recognise this type of illumina probe id. Can anybody help?
I'm sorry that the annotation file we currently supply for Illumina arrays is out-of-date. We are planning for updated Illumina annotation files sometime in the next two months, but they are not yet ready. In the meantime, you can download annotation from the Illumina website and load it into MeV directly.
yes, thanks, I did that and then also used Illumina12k_sym_BN from the MeV ftp in order to obtain annotation for the BN analysis.
Illumina12k_sym_BN seems to rely on gene symbols for the mapping and this almost works except there are a few gene symbols in the annotation from the illumina web site that aren't in the Illumina12k_sym_BN annotation files
Ok, I'm glad that worked out for you. When we release the new Illumina support files, we should have some new BN annotation files as well.
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