Hi Peter. I haven't looked at this since early 2009 and our motive in making this available as a script (instead of within the aroma.affymetrix package) was simply as an FYI and the code is readily available for others to modify for their needs. You will of course understand that underlying packages change all the time.
On a cursory glance from what you have mentioned below, it seems like the script actually works now problem. Each unit appears to be a "probeset", not a "transcript cluster". I know there was a point (looks like early 2009) where Affymetrix made annotation available at the probeset as well as transcript cluster level, whereas when I built this script there was only transcript cluster. Also, you'll notice my post on BioC: https://stat.ethz.ch/pipermail/bioconductor/2009-July/028893.html ... so, 250k probesets seems about right. You'll notice that BioC now makes available annotation at both levels: http://www.bioconductor.org/packages/release/data/annotation/ (hugene10sttranscriptcluster.db, hugene10stprobeset.db) I'm pretty sure that the 'pd.hugene.1.0.st.v1' package includes information about both probesets and transcript clusters, since oligo::rma() can summarize these chips at both levels. So, it may be an easy modification to make to the script to extract this. Also, you haven't told us what you mean by "aroma.affymetrix will not work with it", so I can't offer much there. Cheers, Mark > I attempted to use the script posted on the site to convert the > pd.hugene.1.0.st.v1 package to a CDF file but it appears not to be > working. The resulting cdf file has too many units and > aroma.affymetrix will not work with it beyond naming the CDF. Are you > aware of any issues? > > source("http://bioinf.wehi.edu.au/folders/mrobinson/aroma/PdInfo2Cdf.R";) > PdInfo2Cdf("pd.hugene.1.0.st.v1", "A1_Affy.CEL", overwrite=TRUE) > > I renamed the resulting binary cdf file and moved it to the appropriate > aroma.affymetrix directory. > > setwd("P:\\ANNOTATION\\aromaAffymetrix") > library(aroma.affymetrix) > chipType <- "HuGene-1_0-st-v1" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r4") > print(cdf) > >> print(cdf) > AffymetrixCdfFile: > Path: annotationData/chipTypes/HuGene-1_0-st-v1 > Filename: HuGene-1_0-st-v1,r4.cdf > Filesize: 51.94MB > Chip type: HuGene-1_0-st-v1,r4 > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 1050x1050 > Number of cells: 1102500 > Number of units: 253002 > Cells per unit: 4.36 > Number of QC units: 0 > > -- > 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 aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en > ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ -- 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 aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
