Question on read.probematix
1
0
Entering edit mode
@gunther-honing-1868
Last seen 9.6 years ago
Dear list, I have a short question on read.probematrix(). I use an Affymetrix hgu133plus2 chip. It has 1164 rows and 1164 columns. Thus I expect 1354896 (=1164*1164) messured intensity points. But reading a cel-file I receive 2 (pm and mm) * 604258 = 1208516 entries. The difference is 146380. Even if I take the QC into account I'm slightly confused. It would be kind if you helped me. Greetings Gunther
hgu133plus2 hgu133plus2 • 623 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States
Gunther H?ning wrote: > Dear list, > > I have a short question on read.probematrix(). > I use an Affymetrix hgu133plus2 chip. It has 1164 rows and 1164 columns. > Thus I expect 1354896 (=1164*1164) messured intensity points. But reading a > cel-file I receive 2 (pm and mm) * 604258 = 1208516 entries. > The difference is 146380. Even if I take the QC into account I'm slightly > confused. If you look at the .tiff file in GCOS you will see that there is a 'checkerboard' of probes that go completely around the outside of the chip. These are used by the affy software to align the scanner, and are scanned, but are neither QC nor expression measuring probes. I believe these make up most of your missing probes. Best, Jim > > It would be kind if you helped me. > > Greetings > > Gunther > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENT

Login before adding your answer.

Traffic: 564 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6