[BioC] Simpleaffy QC & GAPDH ratios
Saroj K Mohapatra
saroj at vt.edu
Fri Jun 12 22:39:06 CEST 2009
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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>>
>>
>>
>
>
>
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