Dear Mr./Mrs. Support: We basically encountered the same situations as Karin, is there any solution for this yet? I'm looking for it. Thanks, Hongmei From: Karin Lagesen <karin.lagesen_at_medisin.uio.no> Date: Sun 28 Jan 2007 - 17:49:13 GMT I am working with a custom chip which does not have mm probes, but which does have negative control probes. I would like to see the results of gcrma adjustment of the probe values. I have thus chosen all of the indices of the negative controls and am trying to use them as described in the gcrma package: The indices are here: > randomprobeindexes[1:5,] ???????x y [1,] 114 117 [2,] 116 117 [3,] 118 117 [4,] 120 117 [5,] 122 117 > I now use them to do gcrma: > bg.adjust.gcrma(newdata, affinity.source="local", type="affinities", NCprobe=randomprobeindexes) Adjusting for optical effect.Error in exprs(abatch)[Index, i] <- exprs(abatch)[Index, i] - min(exprs(abatch)[Index, : ????????NAs are not allowed in subscripted assignments > This is due to this: > mm(newdata)[200:205,] dmso5.CEL mnng5.CEL mock5.CEL uv5.CEL [1,] NA NA NA NA [2,] NA NA NA NA [3,] NA NA NA NA [4,] NA NA NA NA [5,] NA NA NA NA [6,] NA NA NA NA > And: > mmindex(newdata)[200:202] $`AFFX-yel006_5_copy5_at`

Hongmei and Karin Sorry for the delay. I have promised Karin to test this with some real data from Karin but I have been away last week mostly. I will follow up this in a few days. Jean Wu On Fri, 2 Mar 2007, Hongmei Jia wrote: > Dear Mr./Mrs. Support: > > We basically encountered the same situations as Karin, is there any > solution for this yet? I'm looking for it. > > Thanks, > > Hongmei > > > From: Karin Lagesen <karin.lagesen_at_medisin.uio.no> > Date: Sun 28 Jan 2007 - 17:49:13 GMT > > > I am working with a custom chip which does not have mm probes, but which > does have negative control probes. I would like to see the results of gcrma > adjustment of the probe values. > > > I have thus chosen all of the indices of the negative controls and am > trying to use them as described in the gcrma package: > > > The indices are here: > > >> randomprobeindexes[1:5,] > > > ???????x y > [1,] 114 117 > [2,] 116 117 > [3,] 118 117 > [4,] 120 117 > [5,] 122 117 > >> > > > I now use them to do gcrma: > > >> bg.adjust.gcrma(newdata, affinity.source="local", type="affinities", > NCprobe=randomprobeindexes) Adjusting for optical effect.Error in > exprs(abatch)[Index, i] <- exprs(abatch)[Index, i] - > min(exprs(abatch)[Index, : > > > ????????NAs are not allowed in subscripted assignments > > > > This is due to this: > > >> mm(newdata)[200:205,] > dmso5.CEL mnng5.CEL mock5.CEL uv5.CEL > > > [1,] NA NA NA NA > > > [2,] NA NA NA NA > > [3,] NA NA NA NA > > [4,] NA NA NA NA > > [5,] NA NA NA NA > > [6,] NA NA NA NA > > > >> > > > And: > > >> mmindex(newdata)[200:202] > $`AFFX-yel006_5_copy5_at`?[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA NA NA NA NA > > > $`AFFX-yel006_5_copy6_at`?[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA NA NA NA NA > > > $`AFFX-yel006_M_copy1_at`?[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA > NA NA NA NA NA > > >> > > > We do have some mm values on the chip, since there is always one control > set present which does have mm probes with it. This one is required for > affymetrix own purposes. Besides this there are no mm values. which means > that most of the mmindex list just states na, and as shown above, so does > the mm list too. > > > Now, my initial strategy was to try and replace all mm values with zero. > gcrma does not use mm values when negative control indices are given, so > this should, afaik, be ok. However, I am not able to do this, and I think > this is due to me not having any mm indices to use for the replacement. > > > Does any of you have any tips on how to overcome this? > > > TIA, Karin > _________________________________ > Hongmei Jia > BASF Plant Science > 26 Davis Drive > Research Triangle Park, NC > Tel: (919) 547-2546 > Fax: (919)547-2423 > > _______________________________________________ > 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 >