Hi Elizabeth, Thanks. I am trying as you have suggested.
Anguraj On Feb 22, 2010, at 5:13 AM, [email protected] wrote: > So with this cdf, and mergeGroups=TRUE, you are getting estimates of the > "transcript cluster" (basically gene) expression -- this is not individual > transcripts of a gene (i.e. isoform) but Affy's definitions of gene. The > relevant identification is the unitName column (the groupName is > irrelevant and in fact misleading when you have summaries of the unit and > not the group -- its always the first group/exon of the unit/gene, so it > doesn't mean anything here). This is Affy's transcript cluster id. In > terms of what you want to do with the id, you have to rely of Affy's > annotation, for example their NetAffx to find out what a transcript > cluster corresponds to. > Best, > Elizabeth > >> Hi Henrik, >> >> Here are the code and sessioninfo(). >> >> library(aroma.affymetrix) >> verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >> chipType <- "HuEx-1_0-st-v2" >> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="core,A20071112,EP") >> print(cdf) >> cs <- AffymetrixCelSet$byName("GSE16125", cdf=cdf) >> print(cs) >> setCdf(cs,cdf) >> bc <- RmaBackgroundCorrection(cs, tag="core") >> csBC <- process(bc,verbose=verbose) >> qn <- QuantileNormalization(csBC, typesToUpdate="pm") >> print(qn) >> csN <- process(qn, verbose=verbose) >> plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) >> print(plmTr) >> fit(plmTr, verbose=verbose) >> rs <- calculateResiduals(plmTr, verbose=verbose) >> cesTr <- getChipEffectSet(plmTr) >> trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE) >> trFit_m<-matrix(as.numeric(unlist(trFit[,6:41])),nrow=18708,ncol=36) >> >> The code ran successfully and I got the values as follows. >> unitName groupName unit group cell GSM403456_A195-01 GSM403457_A195-03 >> 1 2315251 2315252 1 1 1 18.39242 20.05083 >> 2 2315373 2315374 2 1 3 27.54471 37.94356 >> 3 2315554 2315586 3 1 7 57.07763 87.79183 >> >> I got 18708 rows for the entire transcript. >> >> sessionInfo() >> >> R version 2.10.0 (2009-10-26) >> x86_64-redhat-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] preprocessCore_1.8.0 Biobase_2.6.1 aroma.affymetrix_1.4.0 >> [4] aroma.apd_0.1.7 affxparser_1.18.0 R.huge_0.2.0 >> [7] aroma.core_1.4.0 aroma.light_1.15.1 matrixStats_0.1.9 >> [10] R.rsp_0.3.6 R.filesets_0.7.0 digest_0.4.2 >> [13] R.cache_0.2.0 R.utils_1.3.3 R.oo_1.6.7 >> [16] affy_1.24.2 R.methodsS3_1.1.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.14.0 >> >> >> Thanks, >> >> Anguraj >> >> >> On Feb 21, 2010, at 5:23 PM, Henrik Bengtsson wrote: >> >>> Hi. >>> >>> On Sun, Feb 21, 2010 at 3:24 PM, Anguraj Sadanandam >>> <[email protected]> wrote: >>>> Hi Everyone, >>>> >>>> I have question probably many others using Aroma Affy might have had >>>> the same question. I checked the archive but I couldn't find any >>>> straight forward answer to my question, so I am posting this. >>>> >>>> I used Aroma Affy and successfully processed Human HuEx-1_0-st-v2. I >>>> processed for entire transcript rather than exons. However, I am >>>> struggling to map the group and unit names to gene names. I don't know >>>> if I have to provide any other information. >>> >>> Unit names are defined by the CDF, so which unit names you get depends >>> which CDF you used. Note that the terms 'chip type' and 'CDF' are not >>> the same, cf. Page 'Differences between chip type and chip definition >>> file (CDF)': >>> >>> http://aroma-project.org/definitions/chipTypesAndCDFs. >>> >>> You specified that you've used the 'HuEx-1_0-st-v2' chip type, but you >>> haven't specified which CDF. This is one example why we keep asking >>> everyone to show their scripts and useful verbose output. >>> >>> You are saying you are "struggling", but it is not clear how far >>> you've got and what you have tried this far. Because, I will just >>> point you to the example on Page 'Extract probeset summaries (chip >>> effects) as a data frame': >>> >>> http://aroma-project.org/howtos/extractDataFrame >>> >>> to see if that is a start. Depending on CDF used, that might help >>> you. If you browse the Forum Archives [], you will also find >>> discussions such as: >>> >>> 'questiones about annotations for exon arrays: no gene symbol or >>> refseq id for majority of core probe sets?': >>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/ce307bae170c70e8 >>> >>> 'Questions about annotations': >>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/1f4af7fca4352022 >>> >>> /Henrik >>> >>>> >>>> Please let me know. >>>> >>>> Thanks, >>>> >>>> Anguraj >>>> >>>> -- >>>> When reporting problems on aroma.affymetrix, make sure 1) to run the >>>> latest version of the package, 2) to report the output of sessionInfo() >>>> and traceback(), and 3) to post a complete code example. >>>> >>>> >>>> You received this message because you are subscribed to the Google >>>> Groups "aroma.affymetrix" group. >>>> To post to this group, send email to [email protected] >>>> To unsubscribe from this group, send email to >>>> [email protected] >>>> For more options, visit this group at >>>> http://groups.google.com/group/aroma-affymetrix?hl=en >>> >>> -- >>> When reporting problems on aroma.affymetrix, make sure 1) to run the >>> latest version of the package, 2) to report the output of sessionInfo() >>> and traceback(), and 3) to post a complete code example. >>> >>> >>> You received this message because you are subscribed to the Google >>> Groups "aroma.affymetrix" group. >>> To post to this group, send email to [email protected] >>> To unsubscribe from this group, send email to >>> [email protected] >>> For more options, visit this group at >>> http://groups.google.com/group/aroma-affymetrix?hl=en >> >> -- >> When reporting problems on aroma.affymetrix, make sure 1) to run the >> latest version of the package, 2) to report the output of sessionInfo() >> and traceback(), and 3) to post a complete code example. >> >> >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group. >> To post to this group, send email to [email protected] >> To unsubscribe from this group, send email to >> [email protected] >> For more options, visit this group at >> http://groups.google.com/group/aroma-affymetrix?hl=en > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To post to this group, send email to [email protected] > To unsubscribe from this group, send email to > [email protected] > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. 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