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@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@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@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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>
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