Sorry for not being able to answer your question, but there is a specific place
to seek help on bioconductor package problems:
bioconductor at stat.math.ethz.ch
Good luck.
Best,
Baoqiang
---- Original message ---->Date: Sun, 28 Jan 2007 18:49:13 +0100
>From: Karin Lagesen <karin.lagesen at medisin.uio.no>
>Subject: [R] gcrma and chip without mm values
>To: r-help at stat.math.ethz.ch
>
>
>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
>karin.lagesen at medisin.uio.no
>http://folk.uio.no/karinlag
>
>______________________________________________
>R-help at stat.math.ethz.ch 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.