Hi. On Thu, Dec 8, 2011 at 7:57 AM, xiaowei guan <xwei.g...@gmail.com> wrote: > Thanks very much Henrik for your detailed response. I tried as you > suggested. While I still have another question that, in terms of deriving > the gene centric representative values of the probe sets, is there a > protocol or some existing way/code within aroma to achieve that goal? i.e. 4 > probes sets are corresponding to a gene symbol ABCD, as follows: > > 7892501 > 7892502 > 7892503 > 7892504 > > Will it be possible that a summary value is generated for that gene symbol > ABCD instead of the 4 probes[ets]....Really appreciate your help!
I'm not familiar with the contents of this particular CDF. What you get is defined by the CDF you are using, and in this case it is Affymetrix that defined the CDF. What you can control in aroma is whether you wish to summarize per unit group (="probe set") or per unit (="transcript/gene"). This is done by specifying mergeGroups=FALSE or TRUE when setting up the RmaPlm. You may want to try mergeGroups=TRUE; iff those four probesets corresponds to four unit groups of the same unit, then you will get one combined summary. /Henrik > > best, > Xiaowei > > > On Thu, Dec 1, 2011 at 4:34 PM, Henrik Bengtsson > <henrik.bengts...@aroma-project.org> wrote: >> >> Hi. >> >> On Wed, Nov 30, 2011 at 6:38 PM, xiaowei guan <xwei.g...@gmail.com> wrote: >> > >> > Hello Henrik, >> > >> > May I ask you a question about using the >> > http://www.aroma-project.org/node/38 Vignette to derive the gene centric >> > values for HuGene-1_0-st-v1 array? I follow the command, but it only >> > generated the probe level data.... Is there a way to derive the gene symbol >> > not the probe level data? >> >> The estimates you get from: >> >> ces <- getChipEffectSet(plm) >> gExprs <- extractDataFrame(ces, units=NULL, addNames=TRUE) >> >> are indeed gene-level estimates (not prove-level estimates). There >> are 33,252 units (most of the genes) in the HuGene-1_0-st-v1,r3 CDF. >> >> Pay attention to Mark R's remarks at the end, especially that these >> estimates are not on the log-scale, and you often have to take the log >> in downstream analysis. >> >> > >> > Another question is that is the binary cdf file in the website from >> > hg18? >> >> Don't know. The binary CDF was created as is from the text-based CDF >> from Affymetrix. See if you can find out from the Affymetrix "library >> files" or similar. There are also groups out there that generates >> custom CDFs, which might be more up-to-date or meet your needs better. >> >> > >> > My probe names are as follows... the dimension is 31,252* the number of >> > my samples. >> > >> > 7892501 >> > 7892502 >> > 7892503 >> > 7892504 >> > I am wondering do I need to download the Netaffy probe annotation csv >> > file to derive the data set with only gene symbol? Could you please provide >> > me with some guidance? >> >> Below is what Mark Robinson says: >> >> > There are at least 2 options: >> > 1. Download files from Affy and marry it up. >> > >> > http://www.affymetrix.com/estore/browse/products.jsp?productId=131453&categoryId=35676&productName=GeneChip-Human-Gene-1.0-ST-Array#1_3 >> > Go to [HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 32 (11 >> > MB 07/05/11)] link. >> > 2. Use the BioC package hugene10sttranscriptcluster.db: >> > >> > http://www.bioconductor.org/packages/release/data/annotation/html/hugene10sttranscriptcluster.db.html >> >> Hope this helps >> >> /Henrik >> >> > Thanks very much in advance! >> > >> > best, >> > Xiaowei >> > >> > >> > -- >> > 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 with website http://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go to >> > http://www.aroma-project.org/forum/ >> >> -- >> 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 with website http://www.aroma-project.org/. >> To post to this group, send email to aroma-affymetrix@googlegroups.com >> To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ > > > > > -- > Xiaowei Guan > > Research Assistant > Wood Building G-72, > Department of Epidemiology & Biostatistics, Case School of Medicine, > Case Western Reserve University > 10900 Euclid Avenue, > Cleveland, Ohio 44106 > Phone: (216)-368-5542 > > -- > 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 with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- 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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