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/
