Hi Jean, I'm in a similar situation where I'd like to use gcrma on a PM-only custom Affy chip. How many NCprobes are needed to get a good estimate of the relationship between background and probe sequence? My clients didn't spike-in the polyA controls, but there are only 24 probesets X 11 = 264 probes in all for the polyA controls. This seems like not enough to get a good estimate... I'm trying to find out if any other negative controls were put on the array, but if not, do you have any other suggestions? Thanks, Jenny At 11:17 AM 10/25/2006, Zhijin (Jean) Wu wrote: >Hi, Karen, >You can choose type "affinities" in bg.adjust.gcrma. >You will also need to specify which probes you would consider as negative >controls ("NCprobes") in order to estimate the relationship between >background and probe sequences. If, in your experiment, only a small >fraction of probes >are expected to have specific target (for example, only a small fraction of >genes are expressed), you can use all PM probes as NCprobes if there's >no other choice. > >bg.adjust.gcrma(object, NCprobe= >index.of.your.control.probes,type="affinities") > >Is the hybridization method the same as what's used for standard >GeneChip arrays? If not, you may want to estimate the object >"affinity.info" using your own data instead of the default. In this case >you will either need negative control probes or run an negative control >experiment. > >Jean Wu > >On Wed, 25 Oct 2006, Karen Vranizan wrote: > > > I have a PM-only Affy chip. Is it possible to do gcrma on this > data? Thank you. > > > > Karen Vranizan > > Functional Genomics Lab > > 261A Life Sciences Addition > > Mail Code #3200 > > UC Berkeley, CA 94720-3200 > > > > Phone: 510-642-7520 > > Fax: 510-643-2685 > > email: vranizan at berkeley.edu > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Hi Jenny, Negative controls in the scale of thousands will be necessary. It also depends on the proportion of genes expected to be present. In situations when you can assume only a small proportion of genes are expressed you may use all probes, if there's no other alternative. But if you have already chosen genes you expect to be present in your custom arrays, that may be a problem. On Tue, 14 Nov 2006, Jenny Drnevich wrote: > Hi Jean, > > I'm in a similar situation where I'd like to use gcrma on a PM-only custom > Affy chip. How many NCprobes are needed to get a good estimate of the > relationship between background and probe sequence? My clients didn't > spike-in the polyA controls, but there are only 24 probesets X 11 = 264 > probes in all for the polyA controls. This seems like not enough to get a > good estimate... I'm trying to find out if any other negative controls > were put on the array, but if not, do you have any other suggestions? > > Thanks, > Jenny > > > At 11:17 AM 10/25/2006, Zhijin (Jean) Wu wrote: >> Hi, Karen, >> You can choose type "affinities" in bg.adjust.gcrma. >> You will also need to specify which probes you would consider as negative >> controls ("NCprobes") in order to estimate the relationship between >> background and probe sequences. If, in your experiment, only a small >> fraction of probes >> are expected to have specific target (for example, only a small fraction of >> genes are expressed), you can use all PM probes as NCprobes if there's >> no other choice. >> >> bg.adjust.gcrma(object, NCprobe= >> index.of.your.control.probes,type="affinities") >> >> Is the hybridization method the same as what's used for standard >> GeneChip arrays? If not, you may want to estimate the object >> "affinity.info" using your own data instead of the default. In this case >> you will either need negative control probes or run an negative control >> experiment. >> >> Jean Wu >> >> On Wed, 25 Oct 2006, Karen Vranizan wrote: >> >>> I have a PM-only Affy chip. Is it possible to do gcrma on this >> data? Thank you. >>> >>> Karen Vranizan >>> Functional Genomics Lab >>> 261A Life Sciences Addition >>> Mail Code #3200 >>> UC Berkeley, CA 94720-3200 >>> >>> Phone: 510-642-7520 >>> Fax: 510-643-2685 >>> email: vranizan at berkeley.edu >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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 >