On Thu, Aug 27, 2009 at 10:12 AM, Diya Vaka<[email protected]> wrote: > > Dear Henrik, > > Thank you for the help.Now its running fine.
Good. > > I want to get the top 100 over expressed genes and under expressed > genes from this data. > > So can I use the affy and limma packages for that or is there any > thing specifically in aroma.affymetrix. Please start a new thread with a descriptive subject line (and as detailed question as possible) whenever the question changes. This new question has nothing to do with "Could not locate a file for this chip type"). Your previous message was titled "aroma.affymetrix" (which I changed); go to http://groups.google.com/group/aroma-affymetrix/topics - imagine if all people would write "aroma.affymetrix" in the subject line. So, please spend some time on the subject line. I consider this new question to be answered in thread '"gene-1-0-st-array-analysis" - Discussion' started on Aug 27, 2007 [ http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/9ee424979095c462 ]. Cheers, /Henrik > > Thanks in advance, > > Diya > > On Aug 27, 12:39 am, Henrik Bengtsson <[email protected]> wrote: >> Hi. >> >> >> >> On Wed, Aug 26, 2009 at 12:10 PM, Diya Vaka<[email protected]> wrote: >> >> > Hi all, >> >> > I am trying to analyze MoGene-1_0-st-v1 data and I these are the >> > errors: >> >> > In MoGene-1_0-st-v1 directory I have the MoGene-1_0-st-v1.cdf file and >> > I ran the following commands >> >> > setwd("C:/Documents and Settings/annotationData/chipTypes/MoGene-1_0- >> > st-v1/") >> >> getwd() >> > [1] "C:/Documents and Settings/annotationData/chipTypes/MoGene-1_0-st- >> > v1" >> >> chipType <- "MoGene-1_0-st-v1" >> >> cdf <- AffymetrixCdfFile$fromChipType(chipType) >> >> Not the cause of the problem, but please use byChipType() not >> fromChipType() - who told you to use fromChipType()? >> >> > Error in list(`AffymetrixCdfFile$fromChipType(chipType)` = >> > <environment>, : >> >> > [2009-08-26 13:25:55] Exception: Could not locate a file for this chip >> > type: MoGene-1_0-st-v1 >> > at throw(Exception(...)) >> > at throw.default("Could not locate a file for this chip type: ", >> > paste(c(chipT >> > at throw("Could not locate a file for this chip type: ", paste(c >> > (chipType, tag >> > at byChipType.UnitNamesFile(static, ...) >> > at byChipType(static, ...) >> > at method(static, ...) >> > at AffymetrixCdfFile$fromChipType(chipType) >> >> It is correct that annotation files for the 'MoGene-1_0-st-v1' chip >> type should be located in a directory >> >> annotationData/chipTypes/MoGene-1_0-st-v1/ >> >> but it is also important to understand that this is the path >> aroma.affymetrix uses to look up those files, that is, your working >> directory should not be that directory but, in your case, C:/Documents >> and Settings/. >> >> Here is a troubleshooting script: >> >> library("aroma.affymetrix") >> stopifnot(isDirectory("annotationData")) >> stopifnot(isDirectory("annotationData/chipTypes")) >> stopifnot(isDirectory("annotationData/chipTypes/MoGene-1_0-st-v1/")) >> stopifnot(isFile("annotationData/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1.cdf")) >> >> (the above won't work if you use Windows Shortcut links, but I don't you do). >> >> You can read more on Page 'Setting up annotation files': >> >> http://groups.google.com/group/aroma-affymetrix/web/setup >> >> Hope this helps >> >> Henrik >> >> >> >> > Can anyone help me >> >> > Thanks >> >> > Diya > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
