[BioC] Simpleaffy: how are 3/5 ratios calculated

[Ganiraju Manyam]

Hi yogi,

I didnt do the transformation earlier, but did that after your suggestion.

But then also, i didnt find any correlation between the ratios given
by the "ratios" function annd the probe values given by "qcprobes".

The ratios given qc function are also negative sometimes. I didnt
understannd how the ratio can be negative.

Is there any transformation that has been done by the "ratios"
function in simpleaffy?


Lets say, for one of the chip in my datset

a) qcprobes value of GADPH 3' transcript = 14.91

b) qcprobes value of GADPH 5' transcript = 14.71

after transformation...

2^(14.91) = 30690.57

2^(14.71) = 26824.17

Ratio = 30690.57/26824.17 = 1.14

But the ratio given by "ratios" function is 0.194

Moreover, in cases where 3/5 ratio is lessthan one, the value given
"ratios" function is negatiive.

Is there any transformation that has been done by the "ratios"
function in simpleaffy?

Thanks a lot.

Ganiraju

On Fri, Sep 26, 2008 at 1:30 AM, Yogi Sundaravadanam
<yogi.sundaravadanam at agrf.org.au> wrote:
> Dear Ganiraju,
>
> Since the values stored in the QCStats object have been transformed using the base 2 logarithm ,they have to be transferred back to linear scale before calculation of the ratio. The 3'/5' ratios for the GAPDH gene can be displayed with the following code
>
> (2^data at qc.probes[,4]) / (2^data at qc.probes[,6])
> The corresponding values for the B-Actin gene:
> (2^data at qc.probes[,1]) / (2^data at qc.probes[,3])
>
> Is this what you are doing?
>
> Cheers
> Yogi
>
>
> _______________________
> Please Note: The message is intended only for the addressee. If you receive this message in error please do not publish, distribute, or copy it. Please advise the AGRF by telephone or email, and delete this message from your computer.
>
> -----Original Message-----
> From: Ganiraju Manyam [mailto:ganican at gmail.com]
> Sent: Friday, September 26, 2008 1:12 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Simpleaffy: how are 3/5 ratios calculated
>
> Hello,
>
> I am currently looking at the simpleaffy package for affymetrix data QC.
> I have a question regarding the 3'/5' ratio reported in the graph and by
> the function "ratios"
>
> This ratio is different from the ratio obtained by using the value reported
> by the qcProbes() function and making the division "by hand".
>
> Even I see negative ratios. Using the data from qcProbes(), i guess negative
> ratios are not possible.
>
> Can some expert elaberate the background process going on here?
>
> Thanks for your time.
>
> Ganiraju
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>