Hi.
On Wed, Oct 29, 2008 at 1:03 PM, hailei zhang <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I have 228 paired snp arrays, the platform is snp250k_sty. I following the
> steps which is provied on the aroma website.
> When I runing the step of "Calibration for allelic crosstalk", I meet the
> problem. After I run this commond "csAcc <-process(acc,verbose=log)",I can
> not get the csAcc objec.
>
> Thanks.
>
> Hailei
>
> When runing process function, I got this information:
> List of 2
> $ snps :List of 6
> ..$ A/C: int [1:128036, 1:2] 2624 2678 2704 2706 2822 2840 3108 3180
> 3262 3488 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "A" "C"
> ..$ A/G: int [1:557849, 1:2] 2588 2594 2604 2630 2636 2640 2642 2648
> 2662 2682 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "A" "G"
> ..$ A/T: int [1:103336, 1:2] 2634 2654 2780 2800 2916 3054 3260 3388
> 3586 3622 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "A" "T"
> ..$ C/G: int [1:156296, 1:2] 2572 2714 2730 2740 3006 3016 3030 3080
> 3136 3170 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "C" "G"
> ..$ C/T: int [1:537767, 1:2] 2576 2578 2580 2646 2664 2672 2676 2680
> 2708 2734 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "C" "T"
> ..$ G/T: int [1:118188, 1:2] 2602 2606 2656 2712 2854 2904 2966 2990
> 3004 3040 ...
> .. ..- attr(*, "dimnames")=List of 2
> .. .. ..$ : NULL
> .. .. ..$ : chr [1:2] "G" "T"
> $ nonSNPs: NULL
> - attr(*, "version")= int 1
> 20081029 15:41:17| Reading all probe intensities...
> 20081029 15:41:18| Reading all probe intensities...done
> 20081029 15:41:18| Fitting calibration model...
> 20081029 15:41:18| Allele probe-pair group #1 ('A/C') of 6...
> 20081029 15:41:18| Fitting...
> 20081029 15:41:18| Model/algorithm flavor: sfit
> 20081029 15:41:18| Model parameters:
> List of 3
> $ alpha: num [1:5] 0.1 0.075 0.05 0.03 0.01
> $ q : num 2
> $ Q : num 98
> 20081029 15:41:18| Number of data points: 128036
> Error in solve.default(W) :
> system is computationally singular: reciprocal condition number =
> 3.02973e-25
> 20081029 15:41:19| Fitting...done
> 20081029 15:41:19| Allele probe-pair group #1 ('A/C') of 6...done
> 20081029 15:41:19| Fitting calibration model...done
> 20081029 15:41:19| Array #91
> ('CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_H09_112458') of 228...done
> 20081029 15:41:19| Calibrating 228 arrays...done
> 20081029 15:41:19|Calibrating data set for allelic cross talk...done
Wow, I have run ACC (using the sfit algorithm) on tons of CEL files
and I never observed a singularity problem this far. There is
obviously something with Array #91 that causes the crosstalk estimator
to fail. You could do some simple density plots to see if there is
something funny going on with Array #91, e.g.
# Extract Arrays 91-100
cs2 <- extract(cs, 91:100);
col <- rep("black", nbrOfArrays(cs2));
col[1] <- "red";
plotDensity(cs2, types="pm", col=col, lwd=2, ylim=c(0,0.5));
Does Array #91 ("red") look the same as the others?
What about if you do some spatial plots of the probe intensities? See
http://groups.google.com/group/aroma-affymetrix/web/exploratory-analysis-of-raw-data
for examples. If you use the ArrayExplorer you can specify which
arrays you want to plot, e.g. process(ae, arrays=91:95). Does Array
#91 look peculiar?
If you can zip the
CHAMS_p_Sty31_(CO-124089)_Mapping250K_Sty_H09_112458.CEL file and post
it somewhere where I can download it, I can have a look at it. You can
send me the download details offline to my private address if you want
to.
/Henrik
>
>
> The following is my commonds:
>
> library("aroma.affymetrix")
> chipTypes <- c("Mapping250K_Sty")
> cdfs <- AffymetrixCdfFile$byChipType(chipTypes)
> dataSetName <- "snp_all"
> csRawList <- list();
> pairs <-
> read.table(file="/home/hzhang/aroma/pairs_all.txt",sep="\t",header=T)
> pairs <- as.matrix(pairs)
> dim(pairs)
> cs <- AffymetrixCelSet$byName(dataSetName, chipType=chipTypes);
> stopifnot(all(getNames(cs) %in% pairs));
> csRawList[[chipTypes]] <- cs;
> gis <- getGenomeInformation(cdfs)
> sis <- getSnpInformation(cdfs)
> log <- Arguments$getVerbose(-4,timestamp=TRUE)
> cs <- csRawList[[chipTypes]]
> acc <- AllelicCrosstalkCalibration(cs)
> csAcc <-process(acc,verbose=log)
> ls()
>
> >
>
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