[BioC] gcrma and chip without mm values

[Zhijin (Jean) Wu]

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
>
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