Sorry for not being able to answer your question, but there is a specific place to seek help on bioconductor package problems:
[EMAIL PROTECTED] Good luck. Best, Baoqiang ---- Original message ---- >Date: Sun, 28 Jan 2007 18:49:13 +0100 >From: Karin Lagesen <[EMAIL PROTECTED]> >Subject: [R] gcrma and chip without mm values >To: [email protected] > > >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 >-- >Karin Lagesen, PhD student >[EMAIL PROTECTED] >http://folk.uio.no/karinlag > >______________________________________________ >[email protected] mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
