Yes - try reading the help page ?match for further details. If there are any control probes in your summary object, these will not match up, since they aren't annotated as regular transcripts. Best wishes, Matt > So, the "ord" vector contains the indices within > anno$Array_Address_Id_0 where we find the corresponding elements of > featureNames(summary)? > > In other words (or symbols): > > anno$Array_Address_Id_0[ord[n]] = featureNames(summary)[n] > > I hope I have the index notation correct there. > > On Tue, Sep 21, 2010 at 10:49 PM, Matthew Ritchie <mritchie at="" wehi.edu.au=""> > wrote: >> Hi James, >> >> Something like: >> >> anno = >> read.table("Annotation_Illumina_Human-WG-V3_hg18_V1.0.0_Aug09.txt", >> ? ? ? ? ? ? ? ? ? header=TRUE, sep="\t", as.is=TRUE, quote="", >> fill=TRUE) >> >> ord = match(featureNames(summary), anno$Array_Address_Id_0) >> >> ilmnids = anno$Search_key[ord] >> >> # OR >> ilmnids = anno$Probe_id[ord] # not sure which ILMN_* you require! >> >> should match things up for you. >> >> I assume you are analyzing HT-12 arrays since you have set >> 'imagesPerArray=1'. >> >> Best wishes, >> >> Matt >> >>> I guess I'm struggling with how to "match up" (I'm an R newbie) the >>> ids even if I have the file. ?Is there an example somewhere of how to >>> do this? ?I know this is a stupid question, but I am a Java programmer >>> and I'm just learning R and trying to get my mind around this whole >>> "everything is a vector" approach. :) >>> >>> By the way, I tried reading in the manifest file using the readBGX, >>> but it kept throwing errors, saying something like "link 336 does not >>> contain 28 elements". >>> >>> On Tue, Sep 21, 2010 at 8:24 PM, Matthew Ritchie <mritchie at="" wehi.edu.au=""> >>> wrote: >>>> Hi James, >>>> >>>> If you just wanted to annotate the probes, this could be done in R >>>> using >>>> the annotation package 'illuminaHumanv3BeadID.db' >>>> >>>> If you want to convert the numeric probe IDs to ILMN_* ids, then you >>>> can >>>> use the information in the file >>>> >>>> http://www.compbio.group.cam.ac.uk/Resources/Annotation/final /Annotation_Illumina_Human-WG-V3_hg18_V1.0.0_Aug09.zip >>>> >>>> (unzip, read in >>>> 'Annotation_Illumina_Human-WG-V3_hg18_V1.0.0_Aug09.txt' >>>> and then match up the probe ids in your summary object with the values >>>> in >>>> the 'Array_Address_Id_0' column. ?The corresponding columns in this >>>> file >>>> with ILMN_* ids are either 'Search_Key_0' or 'Probe_Id_0' (entries in >>>> both >>>> start with ILMN_ but end in different numbers - I'm not sure which one >>>> you >>>> are after). ?This information can also be obtained from the manifest >>>> files >>>> at >>>> >>>> http://www.switchtoi.com/annotationfiles.ilmn >>>> >>>> (you will need to select the text version of chip type you are using) >>>> >>>> I hope this helps. ?Best wishes, >>>> >>>> Matt >>>> >>>>> I am trying to get a summarized table from our Illumina data. ?So far >>>>> I >>>> have: >>>>> >>>>> targets = read.table("/home/jcarman/targets.txt", header=TRUE, >>>> as.is=TRUE) detail = >>>>> readIllumina(arrayNames=targets$Id,useImages=FALSE,annoPkg="Huma nv3",targets=targets) >>>> summary=createBeadSummaryData(detail,imagesPerArray=1,method="ill umina") >>>>> >>>>> How do I get the probe ids mapped to the ILMN_* gene ids for my >>>>> output? >>>>> >>>>> sessionInfo() returns: >>>>> >>>>> R version 2.11.1 (2010-05-31) >>>>> x86_64-redhat-linux-gnu >>>>> >>>>> locale: >>>>> ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C >>>>> ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 >>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 >>>>> ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C >>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>> >>>>> other attached packages: >>>>> [1] beadarray_1.16.0 Biobase_2.8.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] hwriter_1.2 ?limma_3.4.4 ?tools_2.11.1 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

Hi James, The search_key ids tend to be more gene-specific. Probes that target the same genes will often share the same Search_key but have different Probe_ids. I prefer to work with the Probe_id as my identifier as probes that target the same gene often behave very differently and you really need to check their annotation carefully before combining them. btw, at the moment there is no automatic way of converting bead-level ids to illumina IDs within beadarray, but we are considering it for future releases. Best, Mark On Wed, Sep 22, 2010 at 4:16 AM, James Carman <james at="" carmanconsulting.com=""> wrote: > What's the difference between "Search_key" and "Probe_id"? ?I want the > ILMN ids that folks would most likely be using. ?I think I saw it > referred to before as the "ILMN Gene" or something like that. > > On Tue, Sep 21, 2010 at 10:49 PM, Matthew Ritchie <mritchie at="" wehi.edu.au=""> wrote: >> Hi James, >> >> Something like: >> >> anno = read.table("Annotation_Illumina_Human-WG- V3_hg18_V1.0.0_Aug09.txt", >> ? ? ? ? ? ? ? ? ? header=TRUE, sep="\t", as.is=TRUE, quote="", fill=TRUE) >> >> ord = match(featureNames(summary), anno$Array_Address_Id_0) >> >> ilmnids = anno$Search_key[ord] >> >> # OR >> ilmnids = anno$Probe_id[ord] # not sure which ILMN_* you require! >> >> should match things up for you. >> >> I assume you are analyzing HT-12 arrays since you have set >> 'imagesPerArray=1'. >> >> Best wishes, >> >> Matt >> >>> I guess I'm struggling with how to "match up" (I'm an R newbie) the >>> ids even if I have the file. ?Is there an example somewhere of how to >>> do this? ?I know this is a stupid question, but I am a Java programmer >>> and I'm just learning R and trying to get my mind around this whole >>> "everything is a vector" approach. :) >>> >>> By the way, I tried reading in the manifest file using the readBGX, >>> but it kept throwing errors, saying something like "link 336 does not >>> contain 28 elements". >>> >>> On Tue, Sep 21, 2010 at 8:24 PM, Matthew Ritchie <mritchie at="" wehi.edu.au=""> >>> wrote: >>>> Hi James, >>>> >>>> If you just wanted to annotate the probes, this could be done in R using >>>> the annotation package 'illuminaHumanv3BeadID.db' >>>> >>>> If you want to convert the numeric probe IDs to ILMN_* ids, then you can >>>> use the information in the file >>>> >>>> http://www.compbio.group.cam.ac.uk/Resources/Annotation/final /Annotation_Illumina_Human-WG-V3_hg18_V1.0.0_Aug09.zip >>>> >>>> (unzip, read in 'Annotation_Illumina_Human-WG- V3_hg18_V1.0.0_Aug09.txt' >>>> and then match up the probe ids in your summary object with the values >>>> in >>>> the 'Array_Address_Id_0' column. ?The corresponding columns in this file >>>> with ILMN_* ids are either 'Search_Key_0' or 'Probe_Id_0' (entries in >>>> both >>>> start with ILMN_ but end in different numbers - I'm not sure which one >>>> you >>>> are after). ?This information can also be obtained from the manifest >>>> files >>>> at >>>> >>>> http://www.switchtoi.com/annotationfiles.ilmn >>>> >>>> (you will need to select the text version of chip type you are using) >>>> >>>> I hope this helps. ?Best wishes, >>>> >>>> Matt >>>> >>>>> I am trying to get a summarized table from our Illumina data. ?So far I >>>> have: >>>>> >>>>> targets = read.table("/home/jcarman/targets.txt", header=TRUE, >>>> as.is=TRUE) detail = >>>>> readIllumina(arrayNames=targets$Id,useImages=FALSE,annoPkg="Huma nv3",targets=targets) >>>> summary=createBeadSummaryData(detail,imagesPerArray=1,method="ill umina") >>>>> >>>>> How do I get the probe ids mapped to the ILMN_* gene ids for my output? >>>>> >>>>> sessionInfo() returns: >>>>> >>>>> R version 2.11.1 (2010-05-31) >>>>> x86_64-redhat-linux-gnu >>>>> >>>>> locale: >>>>> ?[1] LC_CTYPE=en_US.utf8 ? ? ? LC_NUMERIC=C >>>>> ?[3] LC_TIME=en_US.utf8 ? ? ? ?LC_COLLATE=en_US.utf8 >>>>> ?[5] LC_MONETARY=C ? ? ? ? ? ? LC_MESSAGES=en_US.utf8 >>>>> ?[7] LC_PAPER=en_US.utf8 ? ? ? LC_NAME=C >>>>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ?LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>> >>>>> other attached packages: >>>>> [1] beadarray_1.16.0 Biobase_2.8.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] hwriter_1.2 ?limma_3.4.4 ?tools_2.11.1 >>>> >>>> >>>> >>>> >>>> >>>> ______________________________________________________________________ >>>> The information in this email is confidential and intend...{{dropped:4}} >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> _______________________________________________ >>> 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 >>> >> >> >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the addressee. >> You must not disclose, forward, print or use it without the permission of the sender. >> ______________________________________________________________________ >> > > _______________________________________________ > 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 >