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
