[BioC] AffyQCReport: "I'm sorry, I do not know about chip type" (celeganscdf)

[Xiwei Wu]

Emmanuel Levy <emmanuel.levy at ...> writes:

> 
> Hello,
> 
> I have an error with affyQCReport:
> Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about
> chip type: celeganscdf
> Error in plot(qc(object)) : unable to find the argument 'x' in
> selecting a method for function 'plot'
> 
> The reason is that the package of the chip I use (celegans) is not
> found in .qcEnv
> 
> Do you know why it is not added when I load the celeganscdf library?
> Shall I add it myself? If yes could you please let me know how?
> 
> Thanks in advance,
> 
> Emmanuel
> 
> > sessionInfo()
> R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
> 
> other attached packages:
>  celeganscdf affyQCReport   simpleaffy   genefilter     survival   reposTools
>     "1.10.0"      "1.8.0"      "2.4.2"      "1.8.0"       "2.20"      "1.8.0"
>         affy      Biobase
>      "1.8.1"      "1.8.0"
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at ...
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 

Hi,

I encountered similar problem while using simpleaffy package for yeast2 chip. 

There is a rather simple way to solve the problem by adding the qc probes
information to the simpleaffy package by yourself, if you can follow the
following instructions:

There are three files in the package subdirectory (sth like
\R\library\simpleaffy\data) defining the chip types that simpleaffy supports.
These are "alpha.tab", which defines the threshold for present/absent call;
"qc.probes.tab", which defines the housekeeping controls, and "spikes.tab",
which defines spike-in controls. These are simply text files that you can edit
using any text editor or excel. 

What you need to do is to add an extra line at the bottom of each file to define
the QC probe ids and alpha parameters. After you've done that, the program
should no long complain about the chip type. 

The following list the first two lines in qc.probes.tab:
"actin3" "actinM" "actin5" "gapdh3" "gapdhM" "gapdh5" "rnapolII3"  "rnapolIIM" 
"rnapolII5" "tatabp3" "tatabpM" "tatabp5"
"atgenomecdf" "AFFX-r2-At-Actin-3_s_at" "AFFX-r2-At-Actin-M_s_at"
"AFFX-r2-At-Actin-5_s_at" "AFFX-Athal-GAPDH_3_s_at" "AFFX-Athal-GAPDH_M_s_at"
"AFFX-Athal-GAPDH_5_s_at" "NA" "NA" "NA" "NA" "NA" "NA"
"ath1121501cdf" "AFFX-r2-At-Actin-3_s_at" "AFFX-r2-At-Actin-M_s_at"
"AFFX-r2-At-Actin-5_s_at" "AFFX-Athal-GAPDH_3_s_at" "AFFX-Athal-GAPDH_M_s_at"
"AFFX-Athal-GAPDH_5_s_at" "NA" "NA" "NA" "NA" "NA" "NA"

You can see that the first column lists the chip name, and the rest lists the
affy probe IDs for the 12 house-keeping controls (actually 6 for most chips,
actin and GAPDH, 3', 5', and M probes for each). All you need to do is to find
out which are the house-keeping probe IDs on your chip and add them to the file.

I added another line for yeast2cdf:  
yeast2cdf	AFFX-YFL039C3_at	AFFX-YFL039CM_at	AFFX-YFL039C5_at	NA	NA	NA
AFFX-YER022w3_at	AFFX-YER022wM_at	AFFX-YER022w5_at	AFFX-YER148w3_at
AFFX-YER148wM_at	AFFX-YER148w5_at

You should also do similar thing for alpha.tab and spikes.tab(the parameter and
probe IDs can be found in GCOS). 

After that, you should reload simpleaffy package, and it won't give any error
messages. 

Hope this helps.

Xiwei Wu
Director, Affymetrix Core Facility
Assistant Research Scientist
Department of Biomedical Informatics
Beckman Research Institute
City of Hope National Medical Center
Duarte, CA 91010