Hi, I have analysed my affy data using an alternative cdf-file (hs133phsense) and would like to obtain an html-table summarizing the results, similar to the output of probes2table. Is there a way to use probes2table even when the input is not a list of affy probeset names? Are there other functions available, similar to probes2table? Many thanks, Ingileif Hallgrimsdottir

Hi Ingileif, Ingileif B. Hallgrimsdottir wrote: > > Hi, > > I have analysed my affy data using an alternative cdf-file > (hs133phsense) and would like to obtain an html-table summarizing the > results, similar to the output of probes2table. Is there a way to use > probes2table even when the input is not a list of affy probeset names? > Are there other functions available, similar to probes2table? Yes, you can use probes2tableBM() which uses biomaRt for the lookup rather than the annotation package. The function arguments are quite similar to probes2table(), but there are some differences, so please see the help page for more info. If you really like the annaffy-style HTML with the green colors on the expression values you could alternatively use the SQLForge functions inside of AnnotationDbi package to build your own annotation.db package which you could then use with probes2table. Best, Jim > > Many thanks, > Ingileif Hallgrimsdottir > > _______________________________________________ > 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, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662