Hi, I think the answer is that MoGene-1_0-st-v1,r3.cdf was created directly from the unofficial Affymetrix ASCII CDF using convertCdf(), as explained on http://aroma-project.org/chipTypes/MoGene-1_0-st-v1/, whereas you creating a CDF based on the annotation available in a Bioconductor Platform Design ("pdInfo") package using PdInfo2Cdf(). The annotations available at the time when Affymetrix and Bioconductor did their work seem to different.
Also, it is likely that Platform Design packages do not contain information on QC units. QC units are artificial/non-biological probesets which are not used in any analysis pipelines that I know of and can be safely ignored. You can search for "Affymetrix QC probesets" to learn more about those few units. Hope this helps, Henrik On Thu, Aug 25, 2011 at 8:47 AM, sabrina <sabrina.s...@gmail.com> wrote: > Hello: > I used PdInfo2Cdf to create my own CDF for Mouse Gene ST 1.0 . > However, when I compared with r3 version available from > aroma.affymetrix, I see a small difference: > > from r3 version > > AffymetrixCdfFile: > Path: annotationData/chipTypes/MoGene-1_0-st-v1 > Filename: MoGene-1_0-st-v1,r3.cdf > Filesize: 17.63MB > Chip type: MoGene-1_0-st-v1,r3 > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 1050x1050 > Number of cells: 1102500 > Number of units: 35512 > Cells per unit: 31.05 > Number of QC units: 1 > > > from my own oversion > > > AffymetrixCdfFile: > Path: annotationData/chipTypes/MoGene-1_0-st-v1 > Filename: MoGene-1_0-st-v1,pd.cdf > Filesize: 17.78MB > Chip type: MoGene-1_0-st-v1,pd > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 1050x1050 > Number of cells: 1102500 > Number of units: 35556 > Cells per unit: 31.01 > Number of QC units: 0 > > ...................................................... > so the number of units is different, so is the number of QC units > > Can someone tell me what the number of QC units is and how did mine > miss that? > > Thanks > > -- > 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/
