[aroma.affymetrix] Re: can't load CDF file
Hi Henrik,
The upload of the cdf file worked now perfectly. Thanks for pointing
out the right version of the supplementary file.
Unfortunately, the upload of the .CEL files still doesn't work? Any
ideas?
cs-AffymetrixCelSet$byName(tissues,cdf=cdf)
Error in list(`AffymetrixCelSet$byName(tissues, cdf = cdf)` =
environment, :
[2010-03-10 13:20:35] Exception: Could not locate a file for this chip
type: MoGene-1_0-st-v1
at throw(Exception(...))
at throw.default(The specified CDF structure (', getChipType(cdf),
') is no
at throw(The specified CDF structure (', getChipType(cdf), ') is
not compat
at setCdf.AffymetrixCelSet(set, cdf)
at setCdf(set, cdf)
at byPath.AffymetrixCelSet(static, path = path, cdf = cdf, ...)
at byPath(static, path = path, cdf = cdf, ...)
at withCallingHandlers(expr, warning = function(w)
invokeRestart(muffleWarnin
at suppressWarnings({
at method(static, ...)
at AffymetrixCelSet$byName(tissues, cdf = cdf)
Many thanks,
Daniela
On Mar 9, 5:12 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi.
On Tue, Mar 9, 2010 at 11:01 PM, dkny169 daniela...@yahoo.com wrote:
Hi Henrik,
I got my documentation from
here:http://bioinf.wehi.edu.au/folders/firmagene/sup3.R
Thanks. That is from the FIRMAGene supplementary materials:
http://bioinf.wehi.edu.au/folders/firmagene/
Mark provides a more up-to-date version:
[04-Feb-2010] Made a modification to the sup3.R script, now available
as sup3_04feb2010.R, to make sure we use the Ensembl annotation that
corresponds to the hg18 (Mar 2006) build.
Mark, would you mind making it more clear on the above URL that
'sup3.R' is out dated? Reversing the NEWS list so that the most
recent events are at the top may help too. Maybe also by renaming the
outdated one sup3.R to sup3_06jun2009.R.
If you could give me a link to a vignette or manual on how to use
FIRMAGene, which is up to date and understandable, I would be more
than thankful!
More comments below...
Many thanks,
Daniela
On Mar 9, 4:56 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi,
please let us know what your source of documentation is, e.g.
webpages, because you are using method names that are either outdated
or non-public. Then I'll answer your questions...
/Henrik
On Tue, Mar 9, 2010 at 10:44 PM, dkny169 daniela...@yahoo.com wrote:
Hi Mark,
Thanks for your answer. I think it works now; I had the working
directory set at chipTypes and not at the parent directory of
annotationData.
I am getting following back:
cdf-AffymetrixCdfFile$findByChipType(MoEx-1_0-st-v1)
cdf
[1] annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf
Don't use findByChipType(), which only returns a pathname, but
byChipType(), which returns an AffymetrixCdfFile object, i.e.
cdf - AffymetrixCdfFile$byChipType(MoEx-1_0-st-v1);
[You did this in your first email, but then all of a sudden
findByChipType(), which is why I wondered where you got that from.]
I am trying to upload the CEL files now that are stored in rawData/
tissues/MoEx-1_0-st-v1. The working directory is set at the parent
directory of rawData. But again I am getting a failure message. What
am I doing wrong now?
cs-AffymetrixCelSet$fromName(tissues,cdf=cdf)
Error in list(`AffymetrixCelSet$fromName(tissues, cdf = cdf)` =
environment, :
[2010-03-09 16:28:12] Exception: AffymetrixCelSet$fromName() is
defunct. Use AffymetrixCelSet$byName() instead.
This error message is clear, ehe?
at throw(Exception(...))
at throw.default(msg)
at throw(msg)
at method(static, ...)
at AffymetrixCelSet$fromName(tissues, cdf = cdf)
cs-AffymetrixCelSet$byName(tissues,cdf=cdf)
Error in list(`AffymetrixCelSet$byName(tissues, cdf = cdf)` =
environment, :
[2010-03-09 16:38:21] Exception: Argument 'cdf' is neither of nor
inherits class AffymetrixCdfFile: character
This one is because you used findByChipType() above; use byChipType()
and it will work.
Hope this helps
Henrik
at throw(Exception(...))
at throw.default(sprintf(Argument '%s' is neither of nor inherits
class %s: %
at throw(sprintf(Argument '%s' is neither of nor inherits class %s:
%s, .nam
at method(static, ...)
at Arguments$getInstanceOf(cdf, AffymetrixCdfFile)
at method(static, ...)
at AffymetrixCelSet$byName(tissues, cdf = cdf)
Thanks,
Daniela
On Mar 9, 3:23 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi Daniela.
Is your CDF in the:
annotationData/chipTypes/MoEx-1_0-st-v1/
directory?
(http://aroma-project.org/node/66)
Cheers,
Mark
Hi,
I stored my CDF file in annotationData/chipTypes; nevertheless I
cannot
upload the file.
Can anyone please tel me what I am doing wrong:
cdf-AffymetrixCdfFile$byChipType(MoEx-1_0-st-v1.cdf)
ror in list(`AffymetrixCdfFile$byChipType(MoEx-1_0-st-v1.cdf)` =
environment, :
Re: [aroma.affymetrix] Re: can't load CDF file
Hi.
On Wed, Mar 10, 2010 at 7:23 PM, dkny169 daniela...@yahoo.com wrote:
Hi Henrik,
The upload of the cdf file worked now perfectly. Thanks for pointing
out the right version of the supplementary file.
Unfortunately, the upload of the .CEL files still doesn't work? Any
ideas?
cs-AffymetrixCelSet$byName(tissues,cdf=cdf)
Error in list(`AffymetrixCelSet$byName(tissues, cdf = cdf)` =
environment, :
[2010-03-10 13:20:35] Exception: Could not locate a file for this chip
type: MoGene-1_0-st-v1
This means that it could not locate any CEL files in the data set
directory. In other words, make sure your CEL files are located in:
rawData/tissues/MoGene-1_0-st-v1/
This is explained on page 'Setup: Location of raw data files':
http://www.aroma-project.org/node/68
Hope this helps
/Henrik
PS. It is called the loading of... or better the setup of..., not
upload of
at throw(Exception(...))
at throw.default(The specified CDF structure (', getChipType(cdf),
') is no
at throw(The specified CDF structure (', getChipType(cdf), ') is
not compat
at setCdf.AffymetrixCelSet(set, cdf)
at setCdf(set, cdf)
at byPath.AffymetrixCelSet(static, path = path, cdf = cdf, ...)
at byPath(static, path = path, cdf = cdf, ...)
at withCallingHandlers(expr, warning = function(w)
invokeRestart(muffleWarnin
at suppressWarnings({
at method(static, ...)
at AffymetrixCelSet$byName(tissues, cdf = cdf)
Many thanks,
Daniela
On Mar 9, 5:12 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi.
On Tue, Mar 9, 2010 at 11:01 PM, dkny169 daniela...@yahoo.com wrote:
Hi Henrik,
I got my documentation from
here:http://bioinf.wehi.edu.au/folders/firmagene/sup3.R
Thanks. That is from the FIRMAGene supplementary materials:
http://bioinf.wehi.edu.au/folders/firmagene/
Mark provides a more up-to-date version:
[04-Feb-2010] Made a modification to the sup3.R script, now available
as sup3_04feb2010.R, to make sure we use the Ensembl annotation that
corresponds to the hg18 (Mar 2006) build.
Mark, would you mind making it more clear on the above URL that
'sup3.R' is out dated? Reversing the NEWS list so that the most
recent events are at the top may help too. Maybe also by renaming the
outdated one sup3.R to sup3_06jun2009.R.
If you could give me a link to a vignette or manual on how to use
FIRMAGene, which is up to date and understandable, I would be more
than thankful!
More comments below...
Many thanks,
Daniela
On Mar 9, 4:56 pm, Henrik Bengtsson henrik.bengts...@gmail.com
wrote:
Hi,
please let us know what your source of documentation is, e.g.
webpages, because you are using method names that are either outdated
or non-public. Then I'll answer your questions...
/Henrik
On Tue, Mar 9, 2010 at 10:44 PM, dkny169 daniela...@yahoo.com wrote:
Hi Mark,
Thanks for your answer. I think it works now; I had the working
directory set at chipTypes and not at the parent directory of
annotationData.
I am getting following back:
cdf-AffymetrixCdfFile$findByChipType(MoEx-1_0-st-v1)
cdf
[1] annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf
Don't use findByChipType(), which only returns a pathname, but
byChipType(), which returns an AffymetrixCdfFile object, i.e.
cdf - AffymetrixCdfFile$byChipType(MoEx-1_0-st-v1);
[You did this in your first email, but then all of a sudden
findByChipType(), which is why I wondered where you got that from.]
I am trying to upload the CEL files now that are stored in rawData/
tissues/MoEx-1_0-st-v1. The working directory is set at the parent
directory of rawData. But again I am getting a failure message. What
am I doing wrong now?
cs-AffymetrixCelSet$fromName(tissues,cdf=cdf)
Error in list(`AffymetrixCelSet$fromName(tissues, cdf = cdf)` =
environment, :
[2010-03-09 16:28:12] Exception: AffymetrixCelSet$fromName() is
defunct. Use AffymetrixCelSet$byName() instead.
This error message is clear, ehe?
at throw(Exception(...))
at throw.default(msg)
at throw(msg)
at method(static, ...)
at AffymetrixCelSet$fromName(tissues, cdf = cdf)
cs-AffymetrixCelSet$byName(tissues,cdf=cdf)
Error in list(`AffymetrixCelSet$byName(tissues, cdf = cdf)` =
environment, :
[2010-03-09 16:38:21] Exception: Argument 'cdf' is neither of nor
inherits class AffymetrixCdfFile: character
This one is because you used findByChipType() above; use byChipType()
and it will work.
Hope this helps
Henrik
at throw(Exception(...))
at throw.default(sprintf(Argument '%s' is neither of nor inherits
class %s: %
at throw(sprintf(Argument '%s' is neither of nor inherits class %s:
%s, .nam
at method(static, ...)
at Arguments$getInstanceOf(cdf, AffymetrixCdfFile)
at method(static, ...)
at AffymetrixCelSet$byName(tissues, cdf = cdf)
Thanks,
Daniela
On Mar 9, 3:23 pm, Mark Robinson mrobin...@wehi.edu.au wrote:
Hi
[aroma.affymetrix] Help with creating a CDF from PDInfoBuilder Library
I'm having some trouble creating a CDF file from the PDInforBuilder library for the HuGene-1_0-st-v1. I want to use the latest r4 pgf and clf files, and the r3 CEL file available from Affy does not have the non-genomic probes. I attempted to follow the instructions at http://www.aroma-project.org/node/41 but first off was getting an error Error in `[.data.frame`(probesets, , cols) : undefined columns selected. When I looked at the vignette I noticed that the probeFile was the probeset.csv and not probe.tab. I changed that and then the next error was that the transFile was not of the correct class ScalarCharacter, and that the coreMPS file was not specified. I fixed that and was able to make the package and install it. However, when I create the CDF file using the PdInfo2Cdf script, the resulting CEL file is much larger than I would expect (53,186 KB) and has 253002 units, as oppose to the 33252 that you get with the old version http://www.aroma-project.org/node/30. Any idea what I did wrong? I used the following code to create the package and install it to my library: library(pdInfoBuilder) baseDir - P:\\ANNOTATION\\AffyAnnotation\\Human\\HuGene-1_0-st-v1 pgf - mkScalar(list.files(baseDir, pattern = .pgf, full.names = TRUE)) clf - mkScalar(list.files(baseDir, pattern = .clf, full.names = TRUE)) prob - mkScalar(list.files(baseDir, pattern = .probeset.csv, full.names = TRUE)) trans - mkScalar(list.files(baseDir, pattern = .transcript.csv, full.names = TRUE)) mpsFile - mkScalar(list.files(baseDir, pattern = .mps, full.names = TRUE)) seed - new(AffyGenePDInfoPkgSeed, pgfFile = pgf, clfFile = clf, probeFile = prob, coreMps = mpsFile, geneArray = TRUE, transFile = trans, version = 1.0.4, chipName = HuGene-1_0-st-v1, manufacturer = Affymetrix, author=Peter White, email=peter.wh...@nationwidechildrens.org, biocViews = AnnotationData, genomebuild=hg19, organism = Human, species = Homo Sapiens, url = http://genomics.nchresearch.org/;) makePdInfoPackage(seed, destDir=.) Closed down R and went to the command prompt, navigated to the appropriate directory: R CMD INSTALL pd.hugene.1.0.st.v1 Next, I attempted to create the CDF file (I took one HuGene ST cel file and put it in the working directory): source(http://bioinf.wehi.edu.au/folders/mrobinson/aroma/PdInfo2Cdf.R;) PdInfo2Cdf(pd.hugene.1.0.st.v1, A1_Affy.CEL, overwrite=TRUE) I renamed the resultin binary cdf file and moved it to the appropriate aroma.affymetrix directory. setwd(P:\\ANNOTATION\\aromaAffymetrix) library(aroma.affymetrix) chipType - HuGene-1_0-st-v1 cdf - AffymetrixCdfFile$byChipType(chipType, tags=r4) print(cdf) print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/HuGene-1_0-st-v1 Filename: HuGene-1_0-st-v1,r4.cdf Filesize: 51.94MB Chip type: HuGene-1_0-st-v1,r4 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 1050x1050 Number of cells: 1102500 Number of units: 253002 Cells per unit: 4.36 Number of QC units: 0 sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grDevices datasets splines graphics stats tcltk utils [8] methods base other attached packages: [1] aroma.affymetrix_1.5.0 aroma.apd_0.1.7affxparser_1.18.0 [4] R.huge_0.2.0 aroma.core_1.5.0 aroma.light_1.15.1 [7] matrixStats_0.1.9 R.rsp_0.3.6R.cache_0.2.0 [10] R.filesets_0.8.0 digest_0.4.2 R.utils_1.3.3 [13] R.oo_1.6.7 R.methodsS3_1.1.0 svSocket_0.9-48 [16] TinnR_1.0.3R2HTML_1.59-1 Hmisc_3.7-0 [19] survival_2.35-8 loaded via a namespace (and not attached): [1] cluster_1.12.1 grid_2.10.1lattice_0.18-3 svMisc_0.9-56 tools_2.10.1 -- 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
