[BioC] simpleaffy problem

[Ariel Chernomoretz]

Hi Crispin,


I tried running the expresso implementation as you suggested
but again I get the same error when applying 'pairwise.comparison'
I tried also with different processing method but with no luck.
Thanks for your attention

Ariel,.

 > setwd("GQ002/tissu_06/CEL")
 > x<-read.affy("covdesc")
 >  x.mas<-call.exprs(x,"mas5-R")
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
12488 ids to be processed
|                    |
|####################|
 > results<-pairwise.comparison(x.mas,"treatment",spots=x)
Getting probe level data...
Computing p-values
Doing PMA Calls
Error in pairwise.comparison(x.mas, "treatment", spots = x) :
	couldn't find function "calls<-"
 >





On 23 août 2004, at 07:36, Crispin Miller wrote:

> Hi Ariel,
> Sorry for taking a few days to reply. I guess the simple answer is that
> I don't know, however, I've not had access to a Mac to test simpleaffy
> on:
>
> http://bioinformatics.picr.man.ac.uk/simpleaffy/index.jsp
>
> my instinct is that this is where the problem lies - the scale factors
> look very odd, and there's a fair amount of C-code interfacing with R
> under the bonnet. I'll try to look into things and let you know what I
> find. In the meantime try:
>
>  x.mas<-call.exprs(x,"mas5-R"), which uses the R implementation in
> expresso instead...
>
> As I said, I've not done any testing on macs so be careful! :-)
> Good luck,
>
> Crispin
>
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ariel
> Chernomoretz
> Sent: 18 August 2004 20:20
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] simpleaffy problem
>
> Hi,
> I am trying to reproduce the simpleaffy vignette examples and found 
> some
> weird behavior:
> I read the cel files
>> setwd("GQ002/tissu_06/CEL")
>> x<-read.affy("covdesc")
>> pData(x)
>                       sample treatment
>   GQ002F01D06C4R1.CEL      1         n
>   GQ002F01D06C4R2.CEL      2         n
>   GQ002F01D06C4R3.CEL      3         n
>   GQ002F02D06C4R1.CEL      4         g
>   GQ002F02D06C4R2.CEL      5         g
>   GQ002F02D06C4R3.CEL      6         g
>
> I get the following when apply  mas5 processing method
>> x.mas<-call.exprs(x,"mas5")
>   Background correcting
>   Retrieving data from AffyBatch...done.
>   Computing expression calls...
>   ......done.
>   scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL
> 8.97428766057367e-15
>   Scale factor for: ./GQ002F01D06C4R2.CEL 8.97428766057367e-15
>   Scale factor for: ./GQ002F01D06C4R3.CEL 8.97428766057367e-15
>   Scale factor for: ./GQ002F02D06C4R1.CEL 8.97428766057367e-15
>   Scale factor for: ./GQ002F02D06C4R2.CEL 8.97428766057367e-15
>   Scale factor for: ./GQ002F02D06C4R3.CEL 8.97428766057367e-15
>
> and the following error message while trying to perform a pairwise
> comparation:
>> results<-pairwise.comparison(x.mas,"treatment",spots=x)
> Getting probe level data...
> Computing p-values
> Doing PMA Calls
> Error in get.fold.change.and.t.test(x, group, members, logged = logged,
>   :
> 	NA/NaN/Inf in foreign function call (arg 1)
>
> Moreover if I read again the same CEL files and repeat the mas5.0
> calculation I get the following new scale factors:
>> xx<-read.affy("covdesc")
>> xx.mas<-call.exprs(xx,"mas5")
>   Background correcting
>   Retrieving data from AffyBatch...done.
>   Computing expression calls...
>   ......done.
>   scaling to a TGT of 100 ...Scale factor for: ./GQ002F01D06C4R1.CEL
> 6.52404421935092e-34
>   Scale factor for: ./GQ002F01D06C4R2.CEL 29644.0460038727
>   Scale factor for: ./GQ002F01D06C4R3.CEL 8.45337767106362e-171
>   Scale factor for: ./GQ002F02D06C4R1.CEL 28417.5423558275
>   Scale factor for: ./GQ002F02D06C4R2.CEL 8.45337767106362e-171
>   Scale factor for: ./GQ002F02D06C4R3.CEL 8.45337767106362e-171
>
> Is there a problem reading the cel files? R is not started in the CEL
> files directory, is that a problem?
>
> I am running R 1.9.0 on Mac OS X 10.3.5
> affy 1.4.30
> simpleaffy 1.2.1
>
> Any help would be apreciated
> Ariel./
>
> Ariel Chernomoretz, Ph.D.
> Centre de recherche du CHUL
> 2705 Blv Laurier, bloc T-367
> Sainte-Foy, Qc
> G1V 4G2
> (418)-525-4444 ext 46339
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Ariel Chernomoretz, Ph.D.
Centre de recherche du CHUL
2705 Blv Laurier, bloc T-367
Sainte-Foy, Qc
G1V 4G2
(418)-525-4444 ext 46339