[BioC] Simpleaffy QC & GAPDH ratios

[Saroj K Mohapatra]

Lana:

You are right. The numbers do seem to be log-ratios.

 > dat=ReadAffy()
 > eset=mas5(dat)
 > myqc=qc(dat)
 > ratios(myqc)
        actin3/actin5 actin3/actinM gapdh3/gapdh5 gapdh3/gapdhM
ac1.CEL     0.2878089     0.2367158    -0.2767954    -0.1206753
ac2.CEL     0.2736803     0.2636448    -0.3175412    -0.1373552

I want to check the gapdh 3/5 ratio numbers. First, I have to find out 
which probe sets?

 > gaps=exprs(eset[grep("Gapdh",featureNames(eset)),])
 > gaps
                           ac1.CEL  ac2.CEL
AFFX-GapdhMur/M32599_3_at 29362.31 43935.84
AFFX-GapdhMur/M32599_5_at 35572.47 54753.06
AFFX-GapdhMur/M32599_M_at 31923.99 48324.46

I calculate the ratio of 3_at against 4_at and log-transform.
 > log2(gaps[1,]/gaps[2,])
   ac1.CEL    ac2.CEL
-0.2767954 -0.3175412

These numbers match with the output of ratios(myqc) third column.

 > sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] mouse4302cdf_2.3.0 simpleaffy_2.18.0  gcrma_2.14.1       
matchprobes_1.14.1
[5] genefilter_1.22.0  survival_2.34-1    affy_1.20.2        
Biobase_2.2.2    

loaded via a namespace (and not attached):
[1] affyio_1.10.1        annotate_1.20.1      AnnotationDbi_1.4.3
[4] DBI_0.2-4            preprocessCore_1.4.0 RSQLite_0.7-1      

Saroj

Lana Schaffer wrote:
> Saroj,
> Thank you for your pdf reference.
> I know what is generally written about these GAPDH ratios, but
> the ratios from Simpleaffy have never made sense.   
> First, these ratios are not the same as the ratios from the Affy
> software or from calculated Mas5.0 ratios.  
> Second, there are not only ratios between 0 and 1, there are also
> negative ratios.
> Third, the only way this makes sense, is that these are log ratios.
>
> Lana 
>
> -----Original Message-----
> From: Saroj K Mohapatra [mailto:saroj at vt.edu] 
> Sent: Friday, June 12, 2009 10:03 AM
> To: Lana Schaffer
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Simpleaffy QC
>
> Hi Lana:
>
> "GAPDH 3':5' values are plotted as circles. According to Affymetrix they
> should be about 1. GAPDH values that are considered potential outliers
> (ratio > 1.25) are coloured red, otherwise they are blue." --
> http://bioinformatics.picr.man.ac.uk/downloads/QCandSimpleaffy.pdf
>
> I think the color of the 'circle' symbol matters more than its actual
> position; red suggests a ratio > 1.25. The x axis labels refer to scale
> factor.
>
> Best,
>
> Saroj
>
> Lana Schaffer wrote:
>   
>> Hi,
>> The plot(qc) command prints a plot of the Affy QC metrics.
>> The GAPDH ratio is a bit confusing because the ratios range from <0 to
>>     
>
>   
>>> 3.  How can the GAPDH ratio be 0?
>>>       
>> Could these values represent log of the ratio?
>>
>> Lana Schaffer
>> Biostatistics/Informatics
>> The Scripps Research Institute
>> DNA Array Core Facility
>> La Jolla, CA 92037
>> (858) 784-2263
>> (858) 784-2994
>> schaffer at scripps.edu
>>
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>>
>>   
>>     
>
>
>