[BioC] qc.stats error with mgu74av2

Crispin Miller CMiller at PICR.man.ac.uk
Tue Feb 3 14:26:17 MET 2004


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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>  
> --------------------------------------------------------
> 
>  
> This email is confidential and intended solely for the use of the
> person(s) ('the intended recipient') to whom it was addressed. Any
views or opinions presented are solely those of the author and do not
necessarily represent those of the Paterson Institute for Cancer
Research or the Christie Hospital NHS Trust. It may contain information
that is privileged & confidential within the meaning of applicable law.
Accordingly any dissemination, distribution, copying, or other use of
this message, or any of its  contents, by any person other than the
intended recipient may constitute a breach of civil or criminal law and
is strictly prohibited. If you are NOT the intended recipient please
contact the sender and dispose of this e-mail as soon as possible.
>  
>
 
--------------------------------------------------------

 
This email is confidential and intended solely for the use\ ...{{dropped}}



More information about the Bioconductor mailing list