Hello Fong, as mentioned earlier, I am reporting the small bug in approxfun, and that should get around the pa.calls problem in future releases. However, I found that as a quick fix, you can simply round your expression-set values to 4 or 5 digits, and then, the problem shouldn't occur anymore. At least, that's what worked for me: example code: ... eset <- rma(raw.data) exprs(eset) <- round(exprs(eset), digits=5) ### or if that does not help, try digits=4 myCalls <- pa.calls(eset) or similar. Best, Sam On 27 August 2010 18:49, Samuel Wuest <wuests at="" tcd.ie=""> wrote: > Hi Fong, > > I have pinpointed the problem to the approxfun-function in the stats > package (so the base-contribution of the R-software). So I have posted > the exact problem onto R-help mailing list and got back some possible > explanation: seems to be a small issue with rounding numbers in > approxfun-function in the stats-package (that is called within the > pa.calls-function) > This has nothing to do with the panp-package but might be a small bug > in a base-level function: > See also: > http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright- ignored-td2338313.html#a2338313 > > I'll double check and file a bug report, so it should be fixed in > coming R-releases. > > That said, the bug only seems to show up when a particular data > structure is present (where you have two very very similar numbers in > negative probeset signals and expression set); I have tried out some > commonly used data and there, everything went fine. > > So the pa.calls function should work fine by default and you would > only very rarely run into the problem. > > I'll keep you posted... > > Best, Sam > > On 25 August 2010 22:08, Fong Chun Chan <fongchun at="" interchange.ubc.ca=""> wrote: >> Hi Sam, >> >> Did you ever figure out how to get around this issue? ?I am having the exact >> same issue when I am running pa.calls on my Expression set. ?I am also running R >> version 2.11.1 myself. >> >> Fong >> >> _______________________________________________ >> 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 >> >> > > > > -- > ----------------------------------------------------- > Samuel Wuest > Smurfit Institute of Genetics > Trinity College Dublin > Dublin 2, Ireland > Phone: +353-1-896 2444 > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > Email: wuests at tcd.ie > ------------------------------------------------------ > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie

Hello Fong, as mentioned earlier, I am reporting the small bug in approxfun, and that should get around the pa.calls problem in future releases. However, I found that as a quick fix, you can simply round your expression-set values to 4 or 5 digits, and then, the problem shouldn't occur anymore. At least, that's what worked for me: example code: ... eset <- rma(raw.data) exprs(eset) <- round(exprs(eset), digits=5) ### or if that does not help, try digits=4 myCalls <- pa.calls(eset) or similar. Best, Sam On 27 August 2010 18:49, Samuel Wuest <wuests at="" tcd.ie=""> wrote: > Hi Fong, > > I have pinpointed the problem to the approxfun-function in the stats > package (so the base-contribution of the R-software). So I have posted > the exact problem onto R-help mailing list and got back some possible > explanation: seems to be a small issue with rounding numbers in > approxfun-function in the stats-package (that is called within the > pa.calls-function) > This has nothing to do with the panp-package but might be a small bug > in a base-level function: > See also: > http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright- ignored-td2338313.html#a2338313 > > I'll double check and file a bug report, so it should be fixed in > coming R-releases. > > That said, the bug only seems to show up when a particular data > structure is present (where you have two very very similar numbers in > negative probeset signals and expression set); I have tried out some > commonly used data and there, everything went fine. > > So the pa.calls function should work fine by default and you would > only very rarely run into the problem. > > I'll keep you posted... > > Best, Sam > > On 25 August 2010 22:08, Fong Chun Chan <fongchun at="" interchange.ubc.ca=""> wrote: >> Hi Sam, >> >> Did you ever figure out how to get around this issue? ?I am having the exact >> same issue when I am running pa.calls on my Expression set. ?I am also running R >> version 2.11.1 myself. >> >> Fong >> >> _______________________________________________ >> 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 >> >> > > > > -- > ----------------------------------------------------- > Samuel Wuest > Smurfit Institute of Genetics > Trinity College Dublin > Dublin 2, Ireland > Phone: +353-1-896 2444 > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > Email: wuests at tcd.ie > ------------------------------------------------------ > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie

Hello Fong, as mentioned earlier, I am reporting the small bug in approxfun, and that should get around the pa.calls problem in future releases. However, I found that as a quick fix, you can simply round your expression-set values to 4 or 5 digits, and then, the problem shouldn't occur anymore. At least, that's what worked for me: example code: ... eset <- rma(raw.data) exprs(eset) <- round(exprs(eset), digits=5) ### or if that does not help, try digits=4 myCalls <- pa.calls(eset) or similar. Best, Sam On 27 August 2010 18:49, Samuel Wuest <wuests at="" tcd.ie=""> wrote: > Hi Fong, > > I have pinpointed the problem to the approxfun-function in the stats > package (so the base-contribution of the R-software). So I have posted > the exact problem onto R-help mailing list and got back some possible > explanation: seems to be a small issue with rounding numbers in > approxfun-function in the stats-package (that is called within the > pa.calls-function) > This has nothing to do with the panp-package but might be a small bug > in a base-level function: > See also: > http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright- ignored-td2338313.html#a2338313 > > I'll double check and file a bug report, so it should be fixed in > coming R-releases. > > That said, the bug only seems to show up when a particular data > structure is present (where you have two very very similar numbers in > negative probeset signals and expression set); I have tried out some > commonly used data and there, everything went fine. > > So the pa.calls function should work fine by default and you would > only very rarely run into the problem. > > I'll keep you posted... > > Best, Sam > > On 25 August 2010 22:08, Fong Chun Chan <fongchun at="" interchange.ubc.ca=""> wrote: >> Hi Sam, >> >> Did you ever figure out how to get around this issue? ?I am having the exact >> same issue when I am running pa.calls on my Expression set. ?I am also running R >> version 2.11.1 myself. >> >> Fong >> >> _______________________________________________ >> 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 >> >> > > > > -- > ----------------------------------------------------- > Samuel Wuest > Smurfit Institute of Genetics > Trinity College Dublin > Dublin 2, Ireland > Phone: +353-1-896 2444 > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > Email: wuests at tcd.ie > ------------------------------------------------------ > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie

Hello Fong, as mentioned earlier, I am reporting the small bug in approxfun, and that should get around the pa.calls problem in future releases. However, I found that as a quick fix, you can simply round your expression-set values to 4 or 5 digits, and then, the problem shouldn't occur anymore. At least, that's what worked for me: example code: ... eset <- rma(raw.data) exprs(eset) <- round(exprs(eset), digits=5) ### or if that does not help, try digits=4 myCalls <- pa.calls(eset) or similar. Best, Sam On 27 August 2010 18:49, Samuel Wuest <wuests at="" tcd.ie=""> wrote: > Hi Fong, > > I have pinpointed the problem to the approxfun-function in the stats > package (so the base-contribution of the R-software). So I have posted > the exact problem onto R-help mailing list and got back some possible > explanation: seems to be a small issue with rounding numbers in > approxfun-function in the stats-package (that is called within the > pa.calls-function) > This has nothing to do with the panp-package but might be a small bug > in a base-level function: > See also: > http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright- ignored-td2338313.html#a2338313 > > I'll double check and file a bug report, so it should be fixed in > coming R-releases. > > That said, the bug only seems to show up when a particular data > structure is present (where you have two very very similar numbers in > negative probeset signals and expression set); I have tried out some > commonly used data and there, everything went fine. > > So the pa.calls function should work fine by default and you would > only very rarely run into the problem. > > I'll keep you posted... > > Best, Sam > > On 25 August 2010 22:08, Fong Chun Chan <fongchun at="" interchange.ubc.ca=""> wrote: >> Hi Sam, >> >> Did you ever figure out how to get around this issue? ?I am having the exact >> same issue when I am running pa.calls on my Expression set. ?I am also running R >> version 2.11.1 myself. >> >> Fong >> >> _______________________________________________ >> 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 >> >> > > > > -- > ----------------------------------------------------- > Samuel Wuest > Smurfit Institute of Genetics > Trinity College Dublin > Dublin 2, Ireland > Phone: +353-1-896 2444 > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > Email: wuests at tcd.ie > ------------------------------------------------------ > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie

Hello Fong, as mentioned earlier, I am reporting the small bug in approxfun, and that should get around the pa.calls problem in future releases. However, I found that as a quick fix, you can simply round your expression-set values to 4 or 5 digits, and then, the problem shouldn't occur anymore. At least, that's what worked for me: example code: ... eset <- rma(raw.data) exprs(eset) <- round(exprs(eset), digits=5) ### or if that does not help, try digits=4 myCalls <- pa.calls(eset) or similar. Best, Sam On 27 August 2010 18:49, Samuel Wuest <wuests at="" tcd.ie=""> wrote: > Hi Fong, > > I have pinpointed the problem to the approxfun-function in the stats > package (so the base-contribution of the R-software). So I have posted > the exact problem onto R-help mailing list and got back some possible > explanation: seems to be a small issue with rounding numbers in > approxfun-function in the stats-package (that is called within the > pa.calls-function) > This has nothing to do with the panp-package but might be a small bug > in a base-level function: > See also: > http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright- ignored-td2338313.html#a2338313 > > I'll double check and file a bug report, so it should be fixed in > coming R-releases. > > That said, the bug only seems to show up when a particular data > structure is present (where you have two very very similar numbers in > negative probeset signals and expression set); I have tried out some > commonly used data and there, everything went fine. > > So the pa.calls function should work fine by default and you would > only very rarely run into the problem. > > I'll keep you posted... > > Best, Sam > > On 25 August 2010 22:08, Fong Chun Chan <fongchun at="" interchange.ubc.ca=""> wrote: >> Hi Sam, >> >> Did you ever figure out how to get around this issue? ?I am having the exact >> same issue when I am running pa.calls on my Expression set. ?I am also running R >> version 2.11.1 myself. >> >> Fong >> >> _______________________________________________ >> 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 >> >> > > > > -- > ----------------------------------------------------- > Samuel Wuest > Smurfit Institute of Genetics > Trinity College Dublin > Dublin 2, Ireland > Phone: +353-1-896 2444 > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > Email: wuests at tcd.ie > ------------------------------------------------------ > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie

Thanks Sam. Your workaround did the trick. Fong On Thu, Sep 9, 2010 at 12:37 AM, Samuel Wuest <wuests@tcd.ie> wrote: > Hello Fong, > > as mentioned earlier, I am reporting the small bug in approxfun, and > that should get around the pa.calls problem in future releases. > However, I found that as a quick fix, you can simply round your > expression-set values to 4 or 5 digits, and then, the problem > shouldn't occur anymore. > > At least, that's what worked for me: > > example code: > > ... > eset <- rma(raw.data) > exprs(eset) <- round(exprs(eset), digits=5) ### or if that does not > help, try digits=4 > myCalls <- pa.calls(eset) > > or similar. > > Best, Sam > > On 27 August 2010 18:49, Samuel Wuest <wuests@tcd.ie> wrote: > > Hi Fong, > > > > I have pinpointed the problem to the approxfun-function in the stats > > package (so the base-contribution of the R-software). So I have posted > > the exact problem onto R-help mailing list and got back some possible > > explanation: seems to be a small issue with rounding numbers in > > approxfun-function in the stats-package (that is called within the > > pa.calls-function) > > This has nothing to do with the panp-package but might be a small bug > > in a base-level function: > > See also: > > > http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright- ignored-td2338313.html#a2338313 > > > > I'll double check and file a bug report, so it should be fixed in > > coming R-releases. > > > > That said, the bug only seems to show up when a particular data > > structure is present (where you have two very very similar numbers in > > negative probeset signals and expression set); I have tried out some > > commonly used data and there, everything went fine. > > > > So the pa.calls function should work fine by default and you would > > only very rarely run into the problem. > > > > I'll keep you posted... > > > > Best, Sam > > > > On 25 August 2010 22:08, Fong Chun Chan <fongchun@interchange.ubc.ca> > wrote: > >> Hi Sam, > >> > >> Did you ever figure out how to get around this issue? I am having the > exact > >> same issue when I am running pa.calls on my Expression set. I am also > running R > >> version 2.11.1 myself. > >> > >> Fong > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > > > > > > > > -- > > ----------------------------------------------------- > > Samuel Wuest > > Smurfit Institute of Genetics > > Trinity College Dublin > > Dublin 2, Ireland > > Phone: +353-1-896 2444 > > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > > Email: wuests@tcd.ie > > ------------------------------------------------------ > > > > > > -- > ----------------------------------------------------- > Samuel Wuest > Smurfit Institute of Genetics > Trinity College Dublin > Dublin 2, Ireland > Phone: +353-1-896 2444 > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > Email: wuests@tcd.ie > ------------------------------------------------------ > [[alternative HTML version deleted]]