[R] gcrma and chip without mm values

[Baoqiang Cao]

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
>
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