Hello,
Here is complete details of my code and encountered same problem.
After creating Directory structure i have run following codes and got the
error as follows:
1. source("http://aroma-project.org/hbLite.R";)
2.hbInstall("aroma.cn")
3. hbInstall("aroma.affymetrix")
setwd("D:/Array Express and GEO Files/Aroma-gse11882")
source("http://bioconductor.org/biocLite.R";)
biocLite()
library(aroma.affymetrix) # load aroma.affymetrix package
library(Biobase) # bioconductor
library(gplots) # CRAN
library(gdata) # CRAN
library(limma) # bioconductor
library(GenomeGraphs) # bioconductor
library(affy) # bioconductor
library(aroma.affymetrix);
verbose<- Arguments$getVerbose(-8, timestamp=TRUE);
chipType<- "HG-U133_Plus_2"
cdf<-
AffymetrixCdfFile('annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf');
print(cdf)
CdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2.cdf
File size: 25.04 MB (26251783 bytes)
Chip type: HG-U133_Plus_2
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1164x1164
Number of cells: 1354896
Number of units: 54675
Cells per unit: 24.78
Number of QC units: 9
cs<- AffymetrixCelSet$byPath("rawData/mine/HG-U133_Plus_2/");
> print(cs)
AffymetrixCelSet:
Name: mine1
Tags:
Path: rawData/mine1/HG-U133_Plus_2
Platform: Affymetrix
Chip type: HG-U133_Plus_2
Number of arrays: 173
Names: GSM300166, GSM300167, GSM300168, ..., GSM350078 [173]
Time period: 2005-10-14 14:20:42 -- 2007-10-24 16:31:19
Total file size: 2235.72MB
RAM: 0.13MB
bc<- RmaBackgroundCorrection(cs);
> print(bc)
Error in readCelHeader(pathname) :
Argument 'filename' should be a single file:
csBC<- process(bc,verbose=verbose);
20140201 18:36:30|Background correcting data set...
Error in readCelHeader(pathname) :
Argument 'filename' should be a single file:
20140201 18:36:35|Background correcting data set...done
20140201 18:36:30|Background correcting data set...
Error in readCelHeader(pathname) :
Argument 'filename' should be a single file:
20140201 18:36:35|Background correcting data set...done
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.light_1.32.0 matrixStats_0.8.14 aroma.affymetrix_2.11.1
[4] affxparser_1.34.0 aroma.core_2.11.3 R.devices_2.8.2
[7] R.filesets_2.3.0 R.utils_1.29.8 R.oo_1.17.0
[10] R.methodsS3_1.6.1 BiocInstaller_1.12.0
loaded via a namespace (and not attached):
[1] aroma.apd_0.4.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.36.0
[5] PSCBS_0.40.3 R.cache_0.9.0 R.huge_0.6.0 R.rsp_0.9.28
[9] tools_3.0.2
> traceback()
27: stop("Argument 'filename' should be a single file: ", paste(filename,
collapse = ", "))
26: readCelHeader(pathname)
25: getHeader.AffymetrixCelFile(this)
24: getHeader(this)
23: getCdf.AffymetrixCelFile(getOneFile(this), ...)
22: getCdf(getOneFile(this), ...)
21: getCdf.AffymetrixCelSet(this)
20: getCdf(this)
19: clearCache.AffymetrixCelSet(object)
18: clearCache(object)
17: clone.GenericDataFileSet(this, clear = TRUE, verbose = FALSE)
16: NextMethod("clone", clear = TRUE, verbose = less(verbose))
15: clone.AffymetrixCelSet(this)
14: clone(this)
13: extract.GenericDataFileSet(dsOut, fullnames, onMissing = onMissing)
12: extract(dsOut, fullnames, onMissing = onMissing)
11: getOutputDataSet.AromaTransform(this, incomplete = TRUE, ...,
verbose = less(verbose, 5), cdf = NA, checkChipType = FALSE)
10: NextMethod(generic = "getOutputDataSet", NA, incomplete = TRUE,
cdf = NA, checkChipType = FALSE, verbose = FALSE)
9: do.call("NextMethod", args)
8: getOutputDataSet.Transform(this, incomplete = TRUE, ..., verbose =
less(verbose,
5))
7: getOutputDataSet(this, incomplete = TRUE, ..., verbose = less(verbose,
5))
6: findFilesTodo.AromaTransform(this, ...)
5: findFilesTodo(this, ...)
4: isDone.AromaTransform(this)
3: isDone(this)
2: process.RmaBackgroundCorrection(bc, verbose = verbose)
1: process(bc, verbose = verbose)
Regards,
Bibhu
On Friday, January 31, 2014 1:54:20 PM UTC+5:30, bibhub...@gmail.com wrote:
>
> Hello sir,
>
> i am getting following error. i am giving session info() and traceback ()
> i have tried many option..differrnt system and file name but all failed
> Please help me .Previously i was able to run sucessfully . But now i am
> facing the problem
>
> > traceback()
> 31: stop("Argument 'filename' should be a single file: ", paste(filename,
> collapse = ", "))
> 30: readCelHeader(pathname)
> 29: getHeader.AffymetrixCelFile(this)
> 28: getHeader(this)
> 27: getCdf.AffymetrixCelFile(getOneFile(this), ...)
> 26: getCdf(getOneFile(this), ...)
> 25: getCdf.AffymetrixCelSet(this)
> 24: getCdf(this)
> 23: clearCache.AffymetrixCelSet(object)
> 22: clearCache(object)
> 21: clone.GenericDataFileSet(this, clear = TRUE, verbose = FALSE)
> 20: NextMethod("clone", clear = TRUE, verbose = less(verbose))
> 19: clone.AffymetrixCelSet(this)
> 18: clone(this)
> 17: extract.GenericDataFileSet(dsOut, fullnames, onMissing = onMissing)
> 16: extract(dsOut, fullnames, onMissing = onMissing)
> 15: getOutputDataSet.AromaTransform(this, incomplete = TRUE, ...,
> verbose = less(verbose, 5), cdf = NA, checkChipType = FALSE)
> 14: NextMethod(generic = "getOutputDataSet", NA, incomplete = TRUE,
> cdf = NA, checkChipType = FALSE, verbose = FALSE)
> 13: do.call("NextMethod", args)
> 12: getOutputDataSet.Transform(this, incomplete = TRUE, ..., verbose =
> less(verbose,
> 5))
> 11: getOutputDataSet(this, incomplete = TRUE, ..., verbose = less(verbose,
> 5))
> 10: findFilesTodo.AromaTransform(this, ...)
> 9: findFilesTodo(this, ...)
> 8: isDone.AromaTransform(this)
> 7: isDone(this)
> 6: sprintf("Is done: %s", isDone(this))
> 5: as.character.AromaTransform(x)
> 4: as.character(x)
> 3: print(as.character(x))
> 2: print.Object(NA)
> 1: print(NA)
> > rs
> Error: object 'rs' not found
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
> [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
> [5] LC_TIME=English_India.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.light_1.32.0 matrixStats_0.8.14
> aroma.affymetrix_2.11.1
> [4] aroma.core_2.11.3 R.devices_2.8.2 R.filesets_2.3.0
>
> [7] R.utils_1.29.1 R.oo_1.17.0 affxparser_1.34.0
>
> [10] R.methodsS3_1.6.1
>
> loaded via a namespace (and not attached):
> [1] aroma.apd_0.4.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.36.0
> [5] PSCBS_0.40.3 R.cache_0.9.2 R.huge_0.6.0 R.rsp_0.9.28
> [9] tools_3.0.2
> >
>
--
--
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 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/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
