Error in readCelHeader(pathname) : Argument 'filename' should be a single file ..

[bibhub...@gmail.com]

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    

>

[Pierre Neuvial]

Hi,

Could you also send a code example that generated this error ? From
what you sent there is no way to know what you did that generated this
error.

Best,

Pierre

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[cwat...@gmail.com]

Hello,
I am a new user and am encountering the same error.

I believe the following commands run without issue:
#Load analysis library.
library("aroma.affymetrix")
#File I/O.
#Load description file.
cdf = AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
print(cdf)
#Load sequence file.
acs= AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
print(acs)
#Get genome information.
gi=getGenomeInformation(cdf)
print(gi)
#Get SNP information.
si=getSnpInformation(cdf)
print(si)
#Load .CEL files.
csR = AffymetrixCelSet$byName("GSE13372", cdf=cdf)
print(csR)

However, an attempt to call:
AllelicCrosstalkCalibration(cs)
or:
doCRMAv2(("GSE13372",chipType="GenomeWideSNP_6,Full")

Gives the following error:
Error in readCelHeader(pathname) :

  Argument 'filename' should be a single file:

Here is the output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      

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_1.29.8          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

Please let me know if you require any additional information. Thank you very much for your time.
Best,
Colin

[bibhub...@gmail.com]

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

[Henrik Bengtsson]

Hi,

thanks for reporting with more details. I see that both of you are
using aroma.core 2.11.1, and it could be that that version is causing
the problem. Try to revert back to aroma.core 2.11.0 (available on
CRAN) as:

install.packages("aroma.core")

Then restart(!) R and retry. Please let me know if this solves it
(because then I'll make sure to not make aroma.core 2.11.1 available
via the current installation scripts).

Henrik

[bibhu prasad]

Hi,

 

aroma.core 2.11.0  is working fine. Thnaks  a Lot

Regards, 

Bibhu

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[Henrik Bengtsson]

Thank you Bibhu, this is helpful. Until the next main release of the
Aroma Framework, I'll try to have hbInstall("aroma.affymetrix") to
avoid picking up the wrong aroma.core version.

/Henrik