mauede at alice.it
2010-May-28 14:49 UTC
[R] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
I executed the following lines several times from a script as well as pasting them in an R shell. Systematically biomaRt is failing. The problem is to extract the 3UTR sequences corresponding to a vector containing 1941 Ensembl Transcript numbers (some are duplicated ... is this s problem ?) Please, find the failing instructions in the following including the ENST vector Any suggestion is welcome. Thank you, Maura> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl')Checking attributes ... ok Checking filters ... ok> genes_map[,"ensembl_transcript_id"][1] "ENST00000262187" "ENST00000296271" "ENST00000346166" "ENST00000381570" [5] "ENST00000381588" "ENST00000399762" "ENST00000270357" "ENST00000283646" [9] "ENST00000314915" "ENST00000356660" "ENST00000395978" "ENST00000395980" [13] "ENST00000395981" "ENST00000395983" "ENST00000395986" "ENST00000418212" [17] "ENST00000420794" "ENST00000438929" "ENST00000439476" "ENST00000273064" [21] "ENST00000296084" "ENST00000355481" "ENST00000359596" "ENST00000355794" [25] "ENST00000389232" "ENST00000373537" "ENST00000397131" "ENST00000397134" [29] "ENST00000397135" "ENST00000397137" "ENST00000432507" "ENST00000451676" [33] "ENST00000261714" "ENST00000302190" "ENST00000372733" "ENST00000260130" [37] "ENST00000413219" "ENST00000424270" "ENST00000447182" "ENST00000343575" [41] "ENST00000374426" "ENST00000374429" "ENST00000307712" "ENST00000398844" [45] "ENST00000396425" "ENST00000396426" "ENST00000239944" "ENST00000479209" [49] "ENST00000484761" "ENST00000258962" "ENST00000423765" "ENST00000374580" [53] "ENST00000229390" "ENST00000344528" "ENST00000392011" "ENST00000409212" [57] "ENST00000389589" "ENST00000425436" "ENST00000483851" "ENST00000262461" [61] "ENST00000316341" "ENST00000369626" "ENST00000276033" "ENST00000392339" [65] "ENST00000392340" "ENST00000392341" "ENST00000355773" "ENST00000234256" [69] "ENST00000448784" "ENST00000380379" "ENST00000245407" "ENST00000215882" [73] "ENST00000265631" "ENST00000416240" "ENST00000367001" "ENST00000489447" [77] "ENST00000295736" "ENST00000380752" "ENST00000280612" "ENST00000236877" [81] "ENST00000191922" "ENST00000424542" "ENST00000432365" "ENST00000020945" [85] "ENST00000396822" "ENST00000262188" "ENST00000356800" "ENST00000392811" [89] "ENST00000348513" "ENST00000324856" "ENST00000457599" "ENST00000249647" [93] "ENST00000349777" "ENST00000397138" "ENST00000215730" "ENST00000329565" [97] "ENST00000337404" "ENST00000367054" "ENST00000367055" "ENST00000327443" [101] "ENST00000426431" "ENST00000222584" "ENST00000262554" "ENST00000337841" [105] "ENST00000216484" "ENST00000360718" "ENST00000389805" "ENST00000265354" [109] "ENST00000332118" "ENST00000256015" "ENST00000320370" "ENST00000431877" [113] "ENST00000322310" "ENST00000339775" "ENST00000348354" "ENST00000218089" [117] "ENST00000371144" "ENST00000371145" "ENST00000371157" "ENST00000371160" [121] "ENST00000264657" "ENST00000389272" "ENST00000404395" "ENST00000300134" [125] "ENST00000300737" "ENST00000316199" "ENST00000372806" "ENST00000263918" [129] "ENST00000242770" "ENST00000367568" "ENST00000367941" "ENST00000448348" [133] "ENST00000225777" "ENST00000011473" "ENST00000455385" "ENST00000371225" [137] "ENST00000320307" "ENST00000368096" "ENST00000368097" "ENST00000040877" [141] "ENST00000267811" "ENST00000333725" "ENST00000343827" "ENST00000438423" [145] "ENST00000246912" "ENST00000346833" "ENST00000435881" "ENST00000309134" [149] "ENST00000361905" "ENST00000361985" "ENST00000204517" "ENST00000310282" [153] "ENST00000397991" "ENST00000467072" "ENST00000486111" "ENST00000442011" [157] "ENST00000260356" "ENST00000265460" "ENST00000278836" "ENST00000266085" [161] "ENST00000265384" "ENST00000348208" "ENST00000377245" "ENST00000314888" [165] "ENST00000346501" "ENST00000397396" "ENST00000397397" "ENST00000397404" [169] "ENST00000397406" "ENST00000397408" "ENST00000397411" "ENST00000399778" [173] "ENST00000409531" "ENST00000421676" "ENST00000322019" "ENST00000379384" [177] "ENST00000377044" "ENST00000377066" "ENST00000412275" "ENST00000226225" [181] "ENST00000333007" "ENST00000221132" "ENST00000276431" "ENST00000347739" [185] "ENST00000245817" "ENST00000374080" "ENST00000445275" "ENST00000269305" [189] "ENST00000359597" "ENST00000396473" "ENST00000419024" "ENST00000420246" [193] "ENST00000445888" "ENST00000455263" "ENST00000267996" "ENST00000288398" [197] "ENST00000317516" "ENST00000334895" "ENST00000358278" "ENST00000403994" [201] "ENST00000360958" "ENST00000378292" "ENST00000312970" "ENST00000323144" [205] "ENST00000330188" "ENST00000368527" "ENST00000368533" "ENST00000300933" [209] "ENST00000344824" "ENST00000267622" "ENST00000166345" "ENST00000223208" [213] "ENST00000231238" "ENST00000234831" "ENST00000256997" "ENST00000444355" [217] "ENST00000323274" "ENST00000367926" "ENST00000252108" "ENST00000262999" [221] "ENST00000310836" "ENST00000394511" "ENST00000260187" "ENST00000313870" [225] "ENST00000054666" "ENST00000263559" "ENST00000373382" "ENST00000395098" [229] "ENST00000382882" "ENST00000225512" "ENST00000264634" "ENST00000474267" [233] "ENST00000216037" "ENST00000344347" "ENST00000297857" "ENST00000395571" [237] "ENST00000300823" "ENST00000337433" "ENST00000413984" "ENST00000454662" [241] "ENST00000358704" "ENST00000366538" "ENST00000263095" "ENST00000373953" [245] "ENST00000318522" "ENST00000402711" "ENST00000321027" "ENST00000345514" [249] "ENST00000357195" "ENST00000341181" "ENST00000394180" "ENST00000394181" [253] "ENST00000394185" "ENST00000437922" "ENST00000448209" "ENST00000331808" [257] "ENST00000333129" "ENST00000371795" "ENST00000341084" "ENST00000395984" [261] "ENST00000398637" "ENST00000439706" "ENST00000256689" "ENST00000296861" [265] "ENST00000227471" "ENST00000330938" "ENST00000296921" "ENST00000314340" [269] "ENST00000376629" "ENST00000376637" "ENST00000400895" "ENST00000452018" [273] "ENST00000374169" "ENST00000374171" "ENST00000247584" "ENST00000372583" [277] "ENST00000372584" "ENST00000429157" "ENST00000316377" "ENST00000402508" [281] "ENST00000403359" "ENST00000423594" "ENST00000430590" "ENST00000374586" [285] "ENST00000178638" "ENST00000344366" "ENST00000264010" "ENST00000300302" [289] "ENST00000379792" "ENST00000439977" "ENST00000486715" "ENST00000288616" [293] "ENST00000316803" "ENST00000351200" "ENST00000337190" "ENST00000327702" [297] "ENST00000344100" "ENST00000347598" "ENST00000399591" "ENST00000399595" [301] "ENST00000399597" "ENST00000399601" "ENST00000399603" "ENST00000399606" [305] "ENST00000399617" "ENST00000399621" "ENST00000399629" "ENST00000399634" [309] "ENST00000399637" "ENST00000399638" "ENST00000399641" "ENST00000399644" [313] "ENST00000399649" "ENST00000399655" "ENST00000402845" "ENST00000356860" [317] "ENST00000287202" "ENST00000345617" "ENST00000271688" "ENST00000368954" [321] "ENST00000317610" "ENST00000337526" "ENST00000357376" "ENST00000357732" [325] "ENST00000394609" "ENST00000394611" "ENST00000402434" "ENST00000404909" [329] "ENST00000405240" "ENST00000261951" "ENST00000393356" "ENST00000252512" [333] "ENST00000433566" "ENST00000434536" "ENST00000342232" "ENST00000319017" [337] "ENST00000367387" "ENST00000367390" "ENST00000263205" "ENST00000292733" [341] "ENST00000357641" "ENST00000317483" "ENST00000468148" "ENST00000370888" [345] "ENST00000394636" "ENST00000270176" "ENST00000420247" "ENST00000372458" [349] "ENST00000344843" "ENST00000245539" "ENST00000317534" "ENST00000320585" [353] "ENST00000457199" "ENST00000316448" "ENST00000222547" "ENST00000356033" [357] "ENST00000405458" "ENST00000409753" "ENST00000249364" "ENST00000342367" [361] "ENST00000449187" "ENST00000479257" "ENST00000361538" "ENST00000380118" [365] "ENST00000380125" "ENST00000465828" "ENST00000306721" "ENST00000347703" [369] "ENST00000303155" "ENST00000335754" "ENST00000296137" "ENST00000289779" [373] "ENST00000335772" "ENST00000368026" "ENST00000263867" "ENST00000409670" [377] "ENST00000409724" "ENST00000265109" "ENST00000397449" "ENST00000428746" [381] "ENST00000324894" "ENST00000358792" "ENST00000303660" "ENST00000409487" [385] "ENST00000370763" "ENST00000371579" "ENST00000245441" "ENST00000324292" [389] "ENST00000382041" "ENST00000389870" "ENST00000453196" "ENST00000308360" [393] "ENST00000338086" "ENST00000403432" "ENST00000252804" "ENST00000362031" [397] "ENST00000396526" "ENST00000396534" "ENST00000374274" "ENST00000301886" [401] "ENST00000352068" "ENST00000377244" "ENST00000374623" "ENST00000418342" [405] "ENST00000308394" "ENST00000393588" "ENST00000298700" "ENST00000345633" [409] "ENST00000369315" "ENST00000369318" "ENST00000369321" "ENST00000369331" [413] "ENST00000393012" "ENST00000452490" "ENST00000333868" "ENST00000348549" [417] "ENST00000283095" "ENST00000309190" "ENST00000325674" "ENST00000341926" [421] "ENST00000359176" "ENST00000361634" "ENST00000395812" "ENST00000395813" [425] "ENST00000341049" "ENST00000265814" "ENST00000360348" "ENST00000396218" [429] "ENST00000422361" "ENST00000443001" "ENST00000290858" "ENST00000412916" [433] "ENST00000265070" "ENST00000369452" "ENST00000341783" "ENST00000349405" [437] "ENST00000447890" "ENST00000454118" "ENST00000270792" "ENST00000374243" [441] "ENST00000058691" "ENST00000372813" "ENST00000341590" "ENST00000343279" [445] "ENST00000395631" "ENST00000399304" "ENST00000296411" "ENST00000227507" [449] "ENST00000360796" "ENST00000403550" "ENST00000407022" "ENST00000421906" [453] "ENST00000433053" "ENST00000261254" "ENST00000336873" "ENST00000398145" [457] "ENST00000402105" "ENST00000411771" "ENST00000346416" "ENST00000452723" [461] "ENST00000373030" "ENST00000373039" "ENST00000353224" "ENST00000378423" [465] "ENST00000378429" "ENST00000253363" "ENST00000361162" "ENST00000217086" [469] "ENST00000344018" "ENST00000338700" "ENST00000437508" "ENST00000440171" [473] "ENST00000254231" "ENST00000326279" "ENST00000397909" "ENST00000264157" [477] "ENST00000295238" "ENST00000296140" "ENST00000292303" "ENST00000343801" [481] "ENST00000400886" "ENST00000445772" "ENST00000321442" "ENST00000296425" [485] "ENST00000394276" "ENST00000217971" "ENST00000381962" "ENST00000377452" [489] "ENST00000375985" "ENST00000375994" "ENST00000275080" "ENST00000310786" [493] "ENST00000324953" "ENST00000413644" "ENST00000415861" "ENST00000324662" [497] "ENST00000373983" "ENST00000394497" "ENST00000450136" "ENST00000007414" [501] "ENST00000261183" "ENST00000393249" "ENST00000393250" "ENST00000446075" [505] "ENST00000222800" "ENST00000366340" "ENST00000417078" "ENST00000423884" [509] "ENST00000437775" "ENST00000316399" "ENST00000336941" "ENST00000352083" [513] "ENST00000396356" "ENST00000410080" "ENST00000450135" "ENST00000219439" [517] "ENST00000434463" "ENST00000301043" "ENST00000395243" "ENST00000395245" [521] "ENST00000413526" "ENST00000422028" "ENST00000447716" "ENST00000450529" [525] "ENST00000324106" "ENST00000324787" "ENST00000393008" "ENST00000469351" [529] "ENST00000496958" "ENST00000338653" "ENST00000419348" "ENST00000421577" [533] "ENST00000443524" "ENST00000451739" "ENST00000339399" "ENST00000234389" [537] "ENST00000011653" "ENST00000249289" "ENST00000339430" "ENST00000405528" [541] "ENST00000413364" "ENST00000303375" "ENST00000261917" "ENST00000351554" [545] "ENST00000395850" "ENST00000415002" "ENST00000418830" "ENST00000426650" [549] "ENST00000437761" "ENST00000445143" "ENST00000355653" "ENST00000262225" [553] "ENST00000303575" "ENST00000258531" "ENST00000369075" "ENST00000232496" [557] "ENST00000379153" "ENST00000361976" "ENST00000318950" "ENST00000398073" [561] "ENST00000245541" "ENST00000351904" "ENST00000261678" "ENST00000344113" [565] "ENST00000358025" "ENST00000441438" "ENST00000458046" "ENST00000265368" [569] "ENST00000313630" "ENST00000347037" "ENST00000356820" "ENST00000367247" [573] "ENST00000367251" "ENST00000367255" "ENST00000367256" "ENST00000367257" [577] "ENST00000423061" "ENST00000448038" "ENST00000319670" "ENST00000359920" [581] "ENST00000343455" "ENST00000393063" "ENST00000299163" "ENST00000442724" [585] "ENST00000335793" "ENST00000311052" "ENST00000396593" "ENST00000254584" [589] "ENST00000396777" "ENST00000254190" "ENST00000375240" "ENST00000375241" [593] "ENST00000375242" "ENST00000308478" "ENST00000422987" "ENST00000451085" [597] "ENST00000367463" "ENST00000341846" "ENST00000341864" "ENST00000338950" [601] "ENST00000344537" "ENST00000397306" "ENST00000273261" "ENST00000315554" [605] "ENST00000337517" "ENST00000344548" "ENST00000400259" "ENST00000303694" [609] "ENST00000262241" "ENST00000361311" "ENST00000377298" "ENST00000317968" [613] "ENST00000318007" "ENST00000380180" "ENST00000437932" "ENST00000268603" [617] "ENST00000338010" "ENST00000352268" "ENST00000394313" "ENST00000413859" [621] "ENST00000287239" "ENST00000368124" "ENST00000368125" "ENST00000304534" [625] "ENST00000355294" "ENST00000367117" "ENST00000225388" "ENST00000426398" [629] "ENST00000265351" "ENST00000219789" "ENST00000268220" "ENST00000257904" [633] "ENST00000257190" "ENST00000261593" "ENST00000399230" "ENST00000216185" [637] "ENST00000403313" "ENST00000429495" "ENST00000265734" "ENST00000424848" [641] "ENST00000278193" "ENST00000216456" "ENST00000325680" "ENST00000373264" [645] "ENST00000373265" "ENST00000242210" "ENST00000381626" "ENST00000396152" [649] "ENST00000405342" "ENST00000409467" "ENST00000228872" "ENST00000374987" [653] "ENST00000368814" "ENST00000007699" "ENST00000256644" "ENST00000336868" [657] "ENST00000251241" "ENST00000287218" "ENST00000342697" "ENST00000448464" [661] "ENST00000375066" "ENST00000334344" "ENST00000340124" "ENST00000440783" [665] "ENST00000317669" "ENST00000376876" "ENST00000218004" "ENST00000367881" [669] "ENST00000288670" "ENST00000409430" "ENST00000301905" "ENST00000225973" [673] "ENST00000303004" "ENST00000354268" "ENST00000359052" "ENST00000394961" [677] "ENST00000457823" "ENST00000375826" "ENST00000287169" "ENST00000308271" [681] "ENST00000421625" "ENST00000397457" "ENST00000366955" "ENST00000284073" [685] "ENST00000322684" "ENST00000238616" "ENST00000374338" "ENST00000278353" [689] "ENST00000338399" "ENST00000370277" "ENST00000353507" "ENST00000354991" [693] "ENST00000289119" "ENST00000483063" "ENST00000298159" "ENST00000341223" [697] "ENST00000309955" "ENST00000341222" "ENST00000423241" "ENST00000440180" [701] "ENST00000374720" "ENST00000367875" "ENST00000367876" "ENST00000360957" [705] "ENST00000418234" "ENST00000335725" "ENST00000393454" "ENST00000374269" [709] "ENST00000374271" "ENST00000259324" "ENST00000372599" "ENST00000372600" [713] "ENST00000301280" "ENST00000347159" "ENST00000376588" "ENST00000421149" [717] "ENST00000302541" "ENST00000444716" "ENST00000284049" "ENST00000330687" [721] "ENST00000394106" "ENST00000340370" "ENST00000234115" "ENST00000403716" [725] "ENST00000409279" "ENST00000409612" "ENST00000357650" "ENST00000370112" [729] "ENST00000223950" "ENST00000382293" "ENST00000382297" "ENST00000382303" [733] "ENST00000308249" "ENST00000367261" "ENST00000304449" "ENST00000371527" [737] "ENST00000332029" "ENST00000354464" "ENST00000489294" "ENST00000304658" [741] "ENST00000319190" "ENST00000374557" "ENST00000374566" "ENST00000395468" [745] "ENST00000340099" "ENST00000263062" "ENST00000373166" "ENST00000320230" [749] "ENST00000240285" "ENST00000216410" "ENST00000372792" "ENST00000372797" [753] "ENST00000372805" "ENST00000270257" "ENST00000391951" "ENST00000414125" [757] "ENST00000368843" "ENST00000297229" "ENST00000373006" "ENST00000295373" [761] "ENST00000345383" "ENST00000346301" "ENST00000380656" "ENST00000376980" [765] "ENST00000369681" "ENST00000347613" "ENST00000360642" "ENST00000291421" [769] "ENST00000373471" "ENST00000381718" "ENST00000381736" "ENST00000375667" [773] "ENST00000375679" "ENST00000398316" "ENST00000492622" "ENST00000377084" [777] "ENST00000311191" "ENST00000389797" "ENST00000389798" "ENST00000295522" [781] "ENST00000233055" "ENST00000245787" "ENST00000262213" "ENST00000318006" [785] "ENST00000264128" "ENST00000370041" "ENST00000361170" "ENST00000255198" [789] "ENST00000336949" "ENST00000378474" "ENST00000457894" "ENST00000341657" [793] "ENST00000433651" "ENST00000317702" "ENST00000313080" "ENST00000389760" [797] "ENST00000260506" "ENST00000271234" "ENST00000283290" "ENST00000295349" [801] "ENST00000377252" "ENST00000274695" "ENST00000378610" "ENST00000397216" [805] "ENST00000368847" "ENST00000329271" "ENST00000367419" "ENST00000211314" [809] "ENST00000275262" 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"ENST00000461494" [1765] "ENST00000470131" "ENST00000473645" "ENST00000497056" "ENST00000280154" [1769] "ENST00000393104" "ENST00000264933" "ENST00000316418" "ENST00000359062" [1773] "ENST00000282077" "ENST00000410055" "ENST00000007708" "ENST00000379162" [1777] "ENST00000441463" "ENST00000005178" "ENST00000369306" "ENST00000373344" [1781] "ENST00000395603" "ENST00000379775" "ENST00000379789" "ENST00000373025" [1785] "ENST00000425343" "ENST00000371084" "ENST00000381967" "ENST00000382771" [1789] "ENST00000316782" "ENST00000335686" "ENST00000380520" "ENST00000380524" [1793] "ENST00000380529" "ENST00000380539" "ENST00000380546" "ENST00000258405" [1797] "ENST00000409304" "ENST00000409840" "ENST00000447280" "ENST00000457690" [1801] "ENST00000262039" "ENST00000373507" "ENST00000373509" "ENST00000290431" [1805] "ENST00000301178" "ENST00000359092" "ENST00000300093" "ENST00000357525" [1809] "ENST00000223127" "ENST00000303958" "ENST00000361621" "ENST00000418604" [1813] "ENST00000376327" "ENST00000324093" "ENST00000322985" "ENST00000378555" [1817] "ENST00000395803" "ENST00000406581" "ENST00000452185" "ENST00000219252" [1821] "ENST00000265302" "ENST00000281321" "ENST00000312527" "ENST00000392580" [1825] "ENST00000264867" "ENST00000379731" "ENST00000299492" "ENST00000300026" [1829] "ENST00000225174" "ENST00000345988" "ENST00000305921" "ENST00000234038" [1833] "ENST00000407025" "ENST00000481195" "ENST00000221138" "ENST00000397308" [1837] "ENST00000406655" "ENST00000335585" "ENST00000382599" "ENST00000337738" [1841] "ENST00000355007" "ENST00000358994" "ENST00000393370" "ENST00000328724" [1845] "ENST00000334743" "ENST00000350249" "ENST00000445439" "ENST00000323055" [1849] "ENST00000394853" "ENST00000394854" "ENST00000012443" "ENST00000361188" [1853] "ENST00000361919" "ENST00000394249" "ENST00000286800" "ENST00000399921" [1857] "ENST00000338193" "ENST00000254101" "ENST00000308677" "ENST00000350356" [1861] "ENST00000295797" "ENST00000370521" "ENST00000357068" "ENST00000257860" [1865] "ENST00000005995" "ENST00000450020" "ENST00000455114" "ENST00000366782" [1869] "ENST00000366783" "ENST00000391872" "ENST00000422240" "ENST00000291041" [1873] "ENST00000349038" "ENST00000350092" "ENST00000356948" "ENST00000394601" [1877] "ENST00000371953" "ENST00000393203" "ENST00000367468" "ENST00000358716" [1881] "ENST00000360310" "ENST00000382422" "ENST00000383657" "ENST00000248594" [1885] "ENST00000407343" "ENST00000435495" "ENST00000306726" "ENST00000355233" [1889] "ENST00000356435" "ENST00000360074" "ENST00000381196" "ENST00000397606" [1893] "ENST00000486161" "ENST00000359947" "ENST00000372413" "ENST00000372414" [1897] "ENST00000438120" "ENST00000418331" "ENST00000440289" "ENST00000368213" [1901] "ENST00000368226" "ENST00000331327" "ENST00000395699" "ENST00000262094" [1905] "ENST00000260056" "ENST00000346213" "ENST00000393860" "ENST00000310653" [1909] "ENST00000336083" "ENST00000358015" "ENST00000327550" "ENST00000338561" [1913] "ENST00000394426" "ENST00000231572" "ENST00000320393" "ENST00000356489" [1917] "ENST00000405409" "ENST00000414461" "ENST00000416721" "ENST00000438146" [1921] "ENST00000449924" "ENST00000348849" "ENST00000394885" "ENST00000230381" [1925] "ENST00000308659" "ENST00000337565" "ENST00000357682" "ENST00000393256" [1929] "ENST00000405953" "ENST00000422765" "ENST00000308639" "ENST00000406246" [1933] "ENST00000272190" "ENST00000252268" "ENST00000337907" "ENST00000377464" [1937] "ENST00000400907" "ENST00000400908" "ENST00000440864" "ENST00000309042" [1941] "ENST00000254325"> genes_seq <- getSequence (id=genes_map[,"ensembl_transcript_id"],type="ensembl_transcript_id",+ seqType="3utr",mart=hmart) Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.>tutti i telefonini TIM! [[alternative HTML version deleted]]
Steve Lianoglou
2010-May-28 15:06 UTC
[R] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
Hi, Two things: 1. You mistakenly posted this to the R-help list, when you should have (and probably meant to) send to the bioconductor list. You might want to repost there if you can't figure out the problem. 2. I just tried your query with 4 transcript IDs (one of them was a duplicate) and it worked fine. Maybe the error you are receiving is actually informative of what your problem is:> Error in value[[3L]](cond) : > ?Request to BioMart web service failed. Verify if you are still connected to the internet. ?Alternatively the BioMart web service is temporarily down.and for some reason you're just having a problem talking to the biomart service itself ... Why not try your query with a small number of ensemble transcript id's to see if that'll work? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact