[R] gcrma and chip without mm values

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

-- 
Karin Lagesen, PhD student
karin.lagesen@medisin.uio.no
http://folk.uio.no/karinlag

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Received on Mon Jan 29 04:54:10 2007

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