[BioC] qc.stats error with mgu74av2

[Crispin Miller]

OK - I think I've fixed it. 
I get identical results on u74 data between the Affy software and
qc.stats...
A new version will appear in devl in the goodness of time :-)

Cherio,
Crispin


-----Original Message-----
From: Crispin Miller 
Sent: 03 February 2004 10:27
To: Dick Beyer
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] qc.stats error with mgu74av2


Hi Dick - sorry - entirely my mistake: I'll fix it and get back to you
;-)
Cheers,
Crispin


-----Original Message-----
From: Dick Beyer [mailto:dbeyer at u.washington.edu] 
Sent: 02 February 2004 17:37
To: Crispin Miller
Subject: RE: [BioC] qc.stats error with mgu74av2


Hi Crispin,

The bug I found was in 1.03.  The problem is in the spikes assignment
line:

    spikes <- cbind(det$call["AFFX-r2-Ec-bioB-3_at", ],
det$call["AFFX-r2-Ec-bioC-3_at", 
        ], det$call["AFFX-r2-Ec-bioD-3_at", ],
det$call["AFFX-r2-P1-cre-3_at", 
        ])
 

I don't believe "AFFX-r2-Ec-bioB-3_at" is on the mgu74av2 chip.

Thanks,
Dick
************************************************************************
*******
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
************************************************************************
*******

On Mon, 2 Feb 2004, Crispin Miller wrote:

> Hi Dick,
> Yup - that was an error in the old version... The newest version on
> the site (1.03) has just the switch you suggest (It only handles 
> murine and human arrays at the moment...):
> 
>   if(n %in% c("hgu133acdf", "hgu133atagcdf", "hgu133bcdf",
> "hgu133plus2cdf", "hgu95acdf",
>               "hgu95av2cdf", "hgu95bcdf", "hgu95ccdf", "hgu95dcdf",
> "hgu95ecdf")) {
>     rats <- 2^cbind((x["AFFX-HUMGAPDH/M33197_3_at",] - 
> x["AFFX-HUMGAPDH/M33197_5_at",]),
>                     (x["AFFX-HUMGAPDH/M33197_3_at",] - 
> x["AFFX-HUMGAPDH/M33197_M_at",]),
>                     (x["AFFX-HSAC07/X00351_3_at",]  - 
> x["AFFX-HSAC07/X00351_5_at",]),
>                     (x["AFFX-HSAC07/X00351_3_at",]  - 
> x["AFFX-HSAC07/X00351_M_at",]));
> 
>   }
>   else {
>     if (n %in% c("mgu74acdf", "mgu74av2cdf", "mgu74bcdf",
> "mgu74bv2cdf", "mgu74ccdf", "mgu74cv2cdf", "moe430acdf", "moe430bcdf",
"mu19kcdf")) {
>       rats <- 2^cbind((x["AFFX-GapdhMur/M32599_3_at",] -
> x["AFFX-GapdhMur/M32599_5_at",]),
>                       (x["AFFX-GapdhMur/M32599_3_at",] - 
> x["AFFX-GapdhMur/M32599_M_at",]),
>                       (x["AFFX-b-ActinMur/M12481_3_at",]  - 
> x["AFFX-b-ActinMur/M12481_5_at",]),
>                      (x["AFFX-b-ActinMur/M12481_3_at",]  - 
> x["AFFX-b-ActinMur/M12481_M_at",]));
>     }
>   
>     else { stop(paste("Sorry - I'm afraid I don't know about the spike

> probes on '",n,"' arrays.")) }
> 
> 
> I've also fixed loads of other little bugs and stuff, so it's most
> definitely a good idea to pull down the latest version...:-)
> 
> Cheers,
> Crispin
> 
> 
> -----Original Message-----
> From: Dick Beyer [mailto:dbeyer at u.washington.edu]
> Sent: 01 February 2004 07:03
> To: Bioconductor
> Subject: [BioC] qc.stats error with mgu74av2
> 
> 
> I have tried to use qc.stats from simpleaffy with mgu74av2 chips:
> 
> qc <- qc.stats(x.raw,x.mas5)
> Getting probe level data...
> Computing p-values
> Doing PMA Calls
> Error in cbind(det$call["AFFX-r2-Ec-bioB-3_at", ],
> det$call["AFFX-r2-Ec-bioC-3_at",  : subscript out of bounds
> 
> I believe AFFX-r2-Ec-bioB-3_at is on the hgu133 chip, but not the
> mgu74av2 chip.  The qc.stats code needs a switch for spikes that is 
> chip dependent?
> 
> Thanks,
> Dick
> **********************************************************************
> **
> *******
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
> 			Seattle, WA 98105-6099 
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
> 
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