Hi Vince.
Yes, getUniqueCdf() *should* inflate the dimensions of the original
CDF. Basically, it is rearranging the probesets so that individual
probes do not match to multiple probesets. To do this, it creates a
CDF with a higher dimension, copying the original physical location to
multiple locations. convertToUnique() takes an AffymetrixCelSet and
copies the data to match the new CDF.
I'm not sure what is going wrong in your analysis. But, as Henrik
says, please tell us how you created the CDF as a starter. You have a
near doubling in the number of probes in your unique CDF to the
original CDF, which obviously is curious in itself. So, a full
explanation of what you've done upstream of this would be useful.
Cheers,
Mark
On 16-Mar-10, at 1:09 AM, Henrik Bengtsson wrote:
Hi,
I leave this one to Mark Robinson who is designed createUniqueCdf()
for AffymetrixCdfFile and is on top of this. Though, in the meanwhile
could you please:
1. Clarify the origin of Mm_PromPR_v02.CDF, because Affymetrix does
not provide an CDF.
2. Make the Mm_PromPR_v02.CDF available to us? If you're happy to
share it (and got the rights), I'm happy to have aroma-project.org to
either link to it or host it.
/Henrik
On Fri, Mar 12, 2010 at 8:04 PM, stvjc <carey...@gmail.com> wrote:
cdfU
AffymetrixCdfFile:
Path: annotationData/chipTypes/Mm_PromPR_v02
Filename: Mm_PromPR_v02,unique.CDF
Filesize: 126.33MB
Chip type: Mm_PromPR_v02,unique
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 3026x3026
Number of cells: 9156676
Number of units: 25373
Cells per unit: 360.88
Number of QC units: 0
cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/Mm_PromPR_v02
Filename: Mm_PromPR_v02.cdf
Filesize: 126.33MB
Chip type: Mm_PromPR_v02
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2166x2166
Number of cells: 4691556
Number of units: 25373
Cells per unit: 184.90
Number of QC units: 0
this leads to (i think)
csU = convertToUnique(csN, verbose=verbose)
20100312 14:02:59|Converting to unique CDF...
20100312 14:02:59| Getting unique CDF...
20100312 14:02:59| Getting unique CDF...done
20100312 14:02:59| Input tags:MN,lm
20100312 14:02:59| Input Path: probeData/Dawn,MN,lm/Mm_PromPR_v02
20100312 14:02:59| Output Path:probeData/Dawn,MN,lm,UNQ/Mm_PromPR_v02
20100312 14:02:59| allTags:MN,lm,UNQ
20100312 14:02:59| Test whether dataset exists
20100312 14:02:59| Reading cell indices from standard CDF...
20100312 14:03:08| Reading cell indices from standard CDF...done
20100312 14:03:08| Reading cell indices list from unique CDF...
20100312 14:03:17| Reading cell indices list from unique CDF...done
20100312 14:03:17| Converting CEL data from standard to unique CDF
for
sample 1 ( 10_BL6_IP_Mmp ) of 8...
20100312 14:03:17| Reading intensity values according to standard
CDF...
Error in readCel(filename, indices = indices, readHeader = FALSE,
readOutliers = FALSE, :
Argument 'indices' contains an element out of range.
20100312 14:03:23| Reading intensity values according to standard
CDF...done
20100312 14:03:23| Converting CEL data from standard to unique CDF
for
sample 1 ( 10_BL6_IP_Mmp ) of 8...done
20100312 14:03:23|Converting to unique CDF...done
sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-02 r51194)
x86_64-apple-darwin9.8.0
locale:
[1] C
attached base packages:
[1] stats graphics grDevices datasets tools utils
methods
[8] base
other attached packages:
[1] gsmoothr_0.1.4 limma_3.3.4
aroma.affymetrix_1.5.0
[4] aroma.apd_0.1.7 affxparser_1.19.6
R.huge_0.2.0
[7] aroma.core_1.5.0 aroma.light_1.15.1
matrixStats_0.1.9
[10] R.rsp_0.3.6 R.cache_0.2.0
R.filesets_0.8.0
[13] R.utils_1.3.3 R.oo_1.6.7
R.methodsS3_1.1.0
[16] weaver_1.13.0 codetools_0.2-2
digest_0.4.2
--
When reporting problems on aroma.affymetrix, make sure 1) to run
the latest version of the package, 2) to report the output of
sessionInfo() and traceback(), and 3) to post a complete code
example.
You received this message because you are subscribed to the Google
Groups "aroma.affymetrix" group.
To post to this group, send email to aroma-
affymet...@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
--
When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of
sessionInfo() and traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google
Groups "aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
------------------------------
______________________________________________________________________
The information in this email is confidential and intended solely for the
addressee.
You must not disclose, forward, print or use it without the permission of the
sender.
______________________________________________________________________
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
