[BioC] gcrma and chip without mm values

Hongmei Jia hongmei.jia at basf.com
Fri Mar 2 22:05:19 CET 2007


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



More information about the Bioconductor mailing list