Hi Paz,

I was able to run the code that you sent me without any trouble.  However, here is the output I get:

FILTERING BY ControlType FLAG
------------------------------------------------------
 PROBES BEFORE FILTERING:  12015
 PROBES AFTER ControlType FILTERING:  11259
 RAW DATA WITHOUT CONTROLS OUT : 11259
------------------------------------------------------

Are you sure you have the right annotation package?  It looks like you might be trying to process some other array (one that has 45,220 "probes before filtering" rather than 12,015) with the same annotation package "hgug4112a.db".  Other packages are available here:

http://www.bioconductor.org/packages/2.8/data/annotation/


--Johannes


From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]
Sent: Monday, August 29, 2011 1:26 PM
To: Freudenberg, Johannes (NIH/NIEHS) [E]
Subject: RE: [BioC] normalization one color microarrays

Step 14 is:
###################################################
### chunk number 14: filter.probes
###################################################
ddFILT=filter.probes(ddNORM,
                control=TRUE,
                wellaboveBG=TRUE,
                isfound=TRUE,
                wellaboveNEG=TRUE,
                sat=TRUE,
                PopnOL=TRUE,
                NonUnifOL=T,
                nas=TRUE,
                limWellAbove=75,
                limISF=75,
                limNEG=75,
                limSAT=75,
                limPopnOL=75,
                limNonUnifOL=75,
                limNAS=100,
                makePLOT=F,annotation.package="hgug4112a.db",flag.counts=T,targets)


I can run the step 13 (Correction background and Normalization).


sessionInfo() says:
R version 2.11.1 (2010-05-31)
i686-pc-linux-gnu

locale:
 [1] LC_CTYPE=es_ES.utf8       LC_NUMERIC=C
 [3] LC_TIME=es_ES.utf8        LC_COLLATE=es_ES.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=es_ES.utf8
 [7] LC_PAPER=es_ES.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] vsn_3.16.0           annotate_1.26.1      hgug4112a.db_2.4.1
 [4] org.Hs.eg.db_2.4.1   RSQLite_0.9-4        DBI_0.2-5
 [7] AnnotationDbi_1.10.2 Biobase_2.8.0        marray_1.26.0
[10] limma_3.4.5

loaded via a namespace (and not attached):
[1] affy_1.26.1           affyio_1.16.0         grid_2.11.1
[4] lattice_0.19-26       preprocessCore_1.10.0 xtable_1.5-6

and specifically in step 14 says:

FILTERING BY ControlType FLAG
------------------------------------------------------
 PROBES BEFORE FILTERING:  45220
 PROBES AFTER ControlType FILTERING:  0
 RAW DATA WITHOUT CONTROLS OUT : 0
------------------------------------------------------
FILTERING BY IsWellAboveBG filterFLAG

    FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove:  75 %
    PROBES BEFORE FILTERING:  0
    PROBES AFTER QC FILTERING:  0
    IsNOTWellAboveBG OUT : 0
------------------------------------------------------
FILTERING BY gIsFound filterFLAG

    FLAG FILTERING OPTIONS - FLAG OK = 1 - limISF:  75 %
    PROBES AFTER gIsFound FILTERING:  0
    IsNOTFound OUT : 0
------------------------------------------------------
Error en if (aux[jj] >= Limit[pos[jj]]) { :
  valor ausente donde TRUE/FALSE es necesario

Thanks,
Paz


________________________________
From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov>
To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl>
CC: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>
Date: Mon, 29 Aug 2011 13:12:42 -0400
Subject: RE: [BioC] normalization one color microarrays
Can you please be more specific?  I'm not really sure what step 14 is.  What exactly doesn't work?

Please provide an example that doesn't work for you and the kind of error messages it produces.  It's also a good idea to provide the output of

> sessionInfo()

when you post a question like this to the list.

--Johannes


From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto:[mailto:verotapia@alumnos.utalca.cl]>
Sent: Monday, August 29, 2011 1:06 PM
To: Freudenberg, Johannes (NIH/NIEHS) [E]
Cc: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>
Subject: RE: [BioC] normalization one color microarrays


 when I work with Agi4x44PreProcess, from step 14 onwards it does not work
________________________________
From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov>
To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl>
CC: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>
Date: Mon, 29 Aug 2011 13:01:46 -0400
Subject: RE: [BioC] normalization one color microarrays
Hi Paz,

I'm not exactly sure what kind of microarrays you are trying to process but I'm guessing you are talking about Agilent 4x44 gene expression arrays.  If that is the case, I would recommend to use the Agi4x44Preprocess package.  You can download this package here:

http://www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.html

or by running the following in R

> source("http://bioconductor.org/biocLite.R")
> biocLite("Agi4x44PreProcess")

This package comes with a nice manual which explains all the steps.  It also has plenty of examples you can try.  You can find the manual here:

http://www.bioconductor.org/packages/2.3/bioc/vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf

I hope this helps for now.  Let me know if you more specific questions.

--Johannes


From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto:[mailto:verotapia@alumnos.utalca.cl]>
Sent: Monday, August 29, 2011 12:25 PM
To: Freudenberg, Johannes (NIH/NIEHS) [E]; bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>; bioconductor-bounces@r-project.org<mailto:bioconductor-bounces@r-project.org>
Subject: RE: [BioC] normalization one color microarrays

Hi,
  but if I make not summarization process, how do I build the set of expression?
> From: johannes.freudenberg@nih.gov<mailto:johannes.freudenberg@nih.gov>
> To: verotapia@alumnos.utalca.cl<mailto:verotapia@alumnos.utalca.cl>
> Date: Wed, 24 Aug 2011 16:17:07 -0400
> Subject: RE: [BioC] normalization one color microarrays
>
> Summarization really only applies to Affymetrix arrays where you have several probes per probeset.
>
> --Johannes
>
>
> -----Original Message-----
> From: Paz Tapia Ramirez [mailto:verotapia@alumnos.utalca.cl]<mailto:[mailto:verotapia@alumnos.utalca.cl]>
> Sent: Wednesday, August 24, 2011 4:09 PM
> To: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>; bioconductor-bounces@r-project.org<mailto:bioconductor-bounces@r-project.org>
> Subject: [BioC] normalization one color microarrays
>
>
>
>
>
>
>
>
>
>
> Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please?
>
> Thks,
> Paz
> [[alternative HTML version deleted]]
>
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