Re: [aroma.affymetrix] Re: Alternatives way to access the mailing list archive
Dear Henrik, Here are mailing archive services that I am aware of: like Nabble [1] or Gmane [2], but I have no idea whether they are accessible from China. They are at least not listed here [3], whereas mail-archive is. Hope this helps, Laurent [1] http://www.nabble.com/ [2] http://gmane.org/ [3] http://en.wikipedia.org/wiki/List_of_websites_blocked_in_the_People's_Republic_of_China On 26 September 2010 21:49, Henrik Bengtsson h...@aroma-project.org wrote: Hi, as a follow up on this one; does anyone know of alternative websites that archives our mailing list? We currently have: http://groups.google.com/group/aroma-affymetrix/topics/ http://www.mail-archive.com/aroma-affymetrix@googlegroups.com/maillist.html More specifically, I'm looking for alternatives that are accessible from within China, and the above seem not to be. It would be great to solve this, because the archive is very useful resource. Thanks Henrik On Tue, Sep 21, 2010 at 9:32 PM, Henrik Bengtsson h...@aroma-project.org wrote: Hi, it has been brought to my attention that the Google Group site, which provides our mailing list and its archive: http://groups.google.com/group/aroma-affymetrix/topics/ is not accessible from/blocked by certain countries. Luckily there are some alternatives by other services providing archives of the mailing list, such as: http://www.mail-archive.com/aroma-affymetrix@googlegroups.com/maillist.html I have added a link to the latter on http://aroma-project.org/forum/ /Henrik -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Respected Dr Bengtsson,
My codes and outputs are as follows:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix)
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.cn)
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Exon Data
chipType - MoEx-1_0-st-v1
cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR)
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
cdf - getCdf(csR)
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc - GcRmaBackgroundCorrection(csR, type=affinities)
print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm,
indicesNegativeControl: NULL, affinities: NULL, type: chr affinities,
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
csB - process(bc, verbose=verbose)
20100927 16:31:40|Background correcting data set...
20100927 16:31:40| Computing probe affinities...
20100927 16:31:40| Computing GCRMA probe affinities for 1257006 units...
20100927 16:31:40| Identify PMs and MMs among the CDF cell indices...
logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode FALSETRUENA's
logical 334476 4931683 0
20100927 16:33:30|MMs are defined as non-PMs
20100927 16:33:30|Number of PMs: 4931683
20100927 16:33:30|Number of MMs: 334476
20100927 16:33:30| Identify PMs and MMs among the CDF cell indices...done
20100927 16:33:30| Reading probe-sequence data...
20100927 16:33:30|Retrieving probe-sequence data...
20100927 16:33:30| Chip type (full): MoEx-1_0-st-v1
20100927 16:33:30| Locating probe-tab file...
20100927 16:33:30| Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = environment,
`process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment,
:
[2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
deprectated (v1) search rules:
at throw(Exception(...))
at throw.default(Found probe-tab file only by means of deprectated (v1
at throw(Found probe-tab file only by means of deprectated (v1) search
at method(static, ...)
at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
at method(static, ...)
at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose)
at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
at bgAdjustGcrma.AffymetrixCelSet(NA, path = probeData/Exon Data,GRBC/
at bgAdjustGcrma(NA, path = probeData/Exon Data,GRBC/MoEx-1_0-st-v1,
at do.call(bgAdjustGcrma, args = args)
at process.GcRmaBackgroundCorrection(
20100927 16:33:30| Locating probe-tab file...done
20100927 16:33:30|Retrieving probe-sequence data...done
20100927 16:33:30| Reading probe-sequence data...done
20100927 16:33:30| Computing GCRMA probe affinities for 1257006
units...done
20100927 16:33:30| Computing probe affinities...done
20100927 16:33:30|Background correcting data set...done
traceback()
17: throw.Exception(Exception(...))
16: throw(Exception(...))
15: throw.default(Found probe-tab file only by means of deprectated (v1)
search rules: ,
pathname)
14: throw(Found probe-tab file only by means of deprectated (v1) search
rules: ,
pathname)
13: method(static, ...)
12: AffymetrixProbeTabFile$findByChipType(chipType, what = what,
...)
11: method(static, ...)
10: AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
less(verbose,
100))
9: getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
verbose)
8: getProbeSequenceData(this, safe = safe, verbose = verbose)
7: computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
verbose = less(verbose))
6: computeAffinities(cdf, paths = probePath, ..., verbose = less(verbose))
5
[aroma.affymetrix] CbsModel parameters
Hi Henrik, I was wondering whether there is a way I can fine tune the behavior of CbsModel. Sometimes the default algorithm produces too many small fragments right next to each other without much separation in mean copy numbers. Is there a way to control how smooth the segmentation results are? Thanks a lot! Best, Kai -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Problem with read CDF files
Hello, You need to be in the directory above annotationData. - Dario. Original message Date: Mon, 27 Sep 2010 16:53:06 -0700 (PDT) From: aroma-affymetrix@googlegroups.com (on behalf of Wero ivansk...@gmail.com) Subject: [aroma.affymetrix] Problem with read CDF files To: aroma.affymetrix aroma-affymetrix@googlegroups.com Cc: ii...@inmegen.gob.mx Hi, I have been trying to read the CDF files for the HuGene-1_0-st-v1 array with aroma.affymetrix and it has been very confuse for me. I have the correct CDF files from the aroma page. The CDF files are in the path: /Library/Frameworks/R.framework/ Versions/2.11/Resources/library/aroma.affymetrix/annotationData/ chipTypes/HuGene-1_0-st-v1. My working directory is: annotationData but I still have this error: # cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3) Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = r3)` = environment, : [2010-09-27 06:14:53] Exception: Could not locate a file for this chip type: HuGene-1_0-st-v1,r3 at throw(Exception(...)) at throw.default(Could not locate a file for this chip type: , pa at throw(Could not locate a file for this chip type: , paste(c(ch at method(static, ...) at AffymetrixCdfFile$byChipType(chipType, tags = r3) ## Also, if I look for the cdf path file in R, it returns NULL pathname - annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf cdf - AffymetrixCdfFile(pathname) Error in list(`AffymetrixCdfFile(pathname)` = environment, `extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile, ` = environment, : [2010-09-27 06:48:54] Exception: Pathname not found: annotationData/ chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.cdf (none of the parent directories [annotationData/chipTypes/HuGene-1_0-st-v1/] exist; current directory is '/Library/Frameworks/R.framework/Versions/2.11/ Resources/library/aroma.affymetrix/annotationData/chipTypes/HuGene-1_0- st-v1') at throw(Exception(...)) at throw.default(Pathname not found: , pathname, reason) at throw(Pathname not found: , pathname, reason) at method(static, ...) at Arguments$getReadablePathname(filename, path = path, mustExist = at GenericDataFile(...) at extend(GenericDataFile(...), AromaMicroarrayDataFile) at AromaMicroarrayDataFile(...) at extend(AromaMicroarrayDataFile(...), c(AffymetrixFile, uses(A at AffymetrixFile(...) at extend(AffymetrixFile(...), AromaChipTypeAnnotationFile) at AromaChipTypeAnnotationFile(...) at extend(AromaChipTypeAnnotationFile(...), c(AffymetrixCdfFile, at Affymetrix In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' pathname - getPathname(cdf) print(pathname) [1] annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st- v1,r3.cdf pathname2 - AffymetrixCdfFile$findByChipType(HuGene-1_0-st-v1, tags=3) print(pathname2) NULL ### This is my sessionInfo() R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] oligoClasses_1.10.0Biobase_2.8.0 [3] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 [5] affxparser_1.20.0 R.huge_0.2.0 [7] aroma.core_1.7.0 aroma.light_1.16.1 [9] matrixStats_0.2.1 R.rsp_0.4.0 [11] R.cache_0.3.0 R.filesets_0.9.0 [13] digest_0.4.2 R.utils_1.5.2 [15] R.oo_1.7.4 oligo_1.12.2 [17] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affyio_1.16.0 Biostrings_2.16.5 DBI_0.2-5 [4] IRanges_1.6.6 preprocessCore_1.10.0 splines_2.11.1 [7] tools_2.11.1 This is my traceback() 6: throw.Exception(Exception(...)) 5: throw(Exception(...)) 4: throw.default(msg) 3: throw(msg) 2: method(static, ...) 1: AffymetrixCdfFile$fromChipType(HuGene-1_0-st-v1, tags = r3) ### I would appreciate any help, thanks!!! Wero. -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia -- 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
Re: [aroma.affymetrix] CbsModel parameters
Hi. On Mon, Sep 27, 2010 at 4:51 PM, Kai wangz...@gmail.com wrote: Hi Henrik, I was wondering whether there is a way I can fine tune the behavior of CbsModel. Sometimes the default algorithm produces too many small fragments right next to each other without much separation in mean copy numbers. Is there a way to control how smooth the segmentation results are? Any additional arguments (in ...) that you pass to process(cbs, ...) will be passed down to the DNAcopy::segment(), which is the function doing the actual segmentation. For more details on how fine tuning the CBS algorithm, see help(segment, package=DNAcopy). You may also want to contact the authors of that method/package. /Henrik Thanks a lot! Best, Kai -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Help needed regarding GCRMA normalization of exon arrays using aroma.affymetrix.....
Hi,
sorry, my mistake. I missed that you already did this.
You are missing the 'MoEx-1_0-st-v1.probe.tab' annotation data file.
You can download it from Affymetrix and you'll find a link to their
support page via http://www.aroma-project.org/chipTypes/MoEx-1_0-st-v1
. Download it (something like MoEx-1_0-st-v1 Probe Sequences,
tabular format (130 MB, 3/19/08)) and place it in
annotationData/chipTypes/MoEx-1_0-st-v1/. You can verify that it is
correct by trying the following:
library(aroma.affymetrix);
ptf - AffymetrixProbeTabFile$byChipType(MoEx-1_0-st-v1);
ptf
AffymetrixProbeTabFile:
Name: MoEx-1_0-st-v1
Tags:
Full name: MoEx-1_0-st-v1
Pathname: annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.probe.tab
File size: 460.47 MB (482839635 bytes)
RAM: 0.01 MB
Number of data rows: NA
Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
'targetStrandedness', 'category'
Number of text lines: NA
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1.cdf
Filesize: 274.30MB
Chip type: MoEx-1_0-st-v1
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 1257006
Cells per unit: 5.21
Number of QC units: 0
If you get that to work, then your script should work.
Let me now if this solved your problem.
/Henrik
On Mon, Sep 27, 2010 at 1:58 PM, Prithish Banerjee
prithish.baner...@gmail.com wrote:
Respected Dr Bengtsson,
My codes and outputs are as follows:
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix)
source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.cn)
verbose - Arguments$getVerbose(-10, timestamp=TRUE);
dataSet - Exon Data
chipType - MoEx-1_0-st-v1
cdf - AffymetrixCdfFile$byChipType(chipType,tags=coreR1,A20080718,MR)
print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/MoEx-1_0-st-v1
Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
Filesize: 30.53MB
Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 17831
Cells per unit: 367.54
Number of QC units: 1
csR - AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
AffymetrixCelSet:
Name: Exon Data
Tags:
Path: rawData/Exon Data/MoEx-1_0-st-v1
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Number of arrays: 7
Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
Total file size: 440.55MB
RAM: 0.01MB
cdf - getCdf(csR)
cdfS - AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc - GcRmaBackgroundCorrection(csR, type=affinities)
print(bc)
GcRmaBackgroundCorrection:
Data set: Exon Data
Input tags:
User tags: *
Asterisk ('*') tags: GRBC
Output tags: GRBC
Number of files: 7 (440.55MB)
Platform: Affymetrix
Chip type: MoEx-1_0-st-v1
Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr pm,
indicesNegativeControl: NULL, affinities: NULL, type: chr affinities,
opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
Is done: FALSE
RAM: 0.00MB
csB - process(bc, verbose=verbose)
20100927 16:31:40|Background correcting data set...
20100927 16:31:40| Computing probe affinities...
20100927 16:31:40| Computing GCRMA probe affinities for 1257006 units...
20100927 16:31:40| Identify PMs and MMs among the CDF cell indices...
logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
Mode FALSE TRUE NA's
logical 334476 4931683 0
20100927 16:33:30| MMs are defined as non-PMs
20100927 16:33:30| Number of PMs: 4931683
20100927 16:33:30| Number of MMs: 334476
20100927 16:33:30| Identify PMs and MMs among the CDF cell indices...done
20100927 16:33:30| Reading probe-sequence data...
20100927 16:33:30| Retrieving probe-sequence data...
20100927 16:33:30| Chip type (full): MoEx-1_0-st-v1
20100927 16:33:30| Locating probe-tab file...
20100927 16:33:30| Chip type: MoEx-1_0-st-v1
Error in list(`process(bc, verbose = verbose)` = environment,
`process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = environment,
:
[2010-09-27 16:33:30] Exception: Found probe-tab file only by means of
deprectated (v1) search rules:
at throw(Exception(...))
at throw.default(Found probe-tab file only by means of deprectated (v1
at throw(Found probe-tab file only by means of deprectated (v1) search
at method(static, ...)
at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
at method(static, ...)
at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
at getProbeSequenceData(this, safe = safe, verbose = verbose
