[aroma.affymetrix] Problem with Total Copy Number Vignette

Hello, I sent an e-mail earlier regarding errors in running the total copy number vignette, but please disregard that as it turns out it was just an issue with the annotation files. Sorry for the inconveniences. However, I've encountered another problem that I'm hoping someone could help me with.

Re: [aroma.affymetrix] re: base pair normalization in CRMAv2

sadly it appears my CDF is square: print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/Ag_SNP_1m520721 Filename: Ag_SNP_1m520721.CDF Filesize: 243.65MB Chip type: Ag_SNP_1m520721 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units:

[aroma.affymetrix] Error in sort.list(pairsToBuild) during AllelicCrosstalkCalibration

Dear Usergrop. while proccessing data from the 5000k Sty array (but not the Nsp set), I receive the folleowing error: acc - AllelicCrosstalkCalibration(csR, model=CRMAv2) csC - process(acc) Error in sort.list(pairsToBuild) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a

[aroma.affymetrix] Re: Error during Total copy number analysis using CRMA v1

Hi Henrik, Yes that is correct, sorry again for the inconveniences. Jack On Jun 7, 12:12 pm, Henrik Bengtsson h...@stat.berkeley.edu wrote: Hi Jack, from your new message '[aroma.affymetrix] Problem with Total Copy Number Vignette': On Mon, Jun 7, 2010 at 3:36 PM, Jack Yu

Re: [aroma.affymetrix] Problem with Total Copy Number Vignette

Hi Jack. On Mon, Jun 7, 2010 at 3:36 PM, Jack Yu j.yu...@gmail.com wrote: Hello, I sent an e-mail earlier regarding errors in running the total copy number vignette, but please disregard that as it turns out it was just an issue with the annotation files. Sorry for the inconveniences. Good.

Re: [aroma.affymetrix] re: base pair normalization in CRMAv2

On Mon, Jun 7, 2010 at 4:45 PM, seth redmond seth.redm...@imperial.ac.uk wrote: sadly it appears my CDF is square: print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/Ag_SNP_1m520721 Filename: Ag_SNP_1m520721.CDF Filesize: 243.65MB Chip type: Ag_SNP_1m520721 RAM: 0.00MB File

Re: [aroma.affymetrix] Error in sort.list(pairsToBuild) during AllelicCrosstalkCalibration

Hi. On Mon, Jun 7, 2010 at 4:41 PM, k o ott4...@gmail.com wrote: Dear Usergrop. while proccessing data from the 5000k Sty array (but not the Nsp set), I receive the folleowing error: acc - AllelicCrosstalkCalibration(csR, model=CRMAv2) csC - process(acc) Error in sort.list(pairsToBuild) :

[aroma.affymetrix] Re: Problem with Total Copy Number Vignette

Hi Henrik, I've ran the entirety of the vignette up to the same point (I did forget to run the fit(plm, verbose=verbose) and the same error persists. The reason I'm using version 1 is because all we need is the raw copy number so we didn't need any of the additional tools/calculations.