Re: [aroma.affymetrix] Error: object 'csC' not found.
I tried your suggestion but it is still not working:
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> # Don't display too many decimals.
> options(digits=4)
>
> cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
File size: 612.27 MiB (642007896 bytes)
Chip type: CytoScanHD_Array
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4
>
> gi <- getGenomeInformation(cdf)
> print(gi)
UgpGenomeInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB2008
Full name: CytoScanHD_Array,na32,hg19,HB2008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB2008.ugp
File size: 13.46 MiB (14111425 bytes)
Chip type: CytoScanHD_Array
>
> si <- getSnpInformation(cdf)
> print(si)
UflSnpInformation:
Name: CytoScanHD_Array
Tags: na32,hg19,HB2008
Full name: CytoScanHD_Array,na32,hg19,HB2008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB2008.ufl
File size: 5.38 MiB (5645047 bytes)
Chip type: CytoScanHD_Array
Number of enzymes: 1
>
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MiB (179217487 bytes)
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: 2008 21:44:22
PSTAffymetrixCytoScanHD_ArrayCytoScanHD_Array.probe_tab409176930beaaa56413608b3f9d9d464a07cddcaeHenrik
Bengtssonhenrik.bengts...@aroma-project.org
Chip type: CytoScanHD_Array
Platform: Affymetrix
>
> csR <- AffymetrixCelSet$byName("CNV", cdf=cdf)
> print(csR)
AffymetrixCelSet:
Name: CNV
Tags:
Path: rawData/CNV/CytoScanHD_Array
Platform: Affymetrix
Chip type: CytoScanHD_Array
Number of arrays: 460
Names: GSM1317174_H050150N-CytoScanHD_515-H050150N,
GSM1317175_H050150T-CytoScanHD_516-H050150T,
GSM1317176_H050154N-CytoScanHD_521-H050154N, ...,
GSM1317635_H112971T-CytoScanHD_831-H112971T [460]
Time period: 2012-03-12 16:49:41 -- 2012-04-05 08:47:43
Total file size: 29.55 GiB
>
> cs <- csR
> par(mar=c(4,4,1,1)+0.1)
> plotDensity(cs, lwd=2, ylim=c(0,0.40))
> acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> print(acc)
AllelicCrosstalkCalibration:
Data set: CNV
Input tags:
User tags: *
Asterisk ('*') tags: ACC,ra,-XY
Output tags: ACC,ra,-XY
Number of files: 460 (29.55 GiB)
Platform: Affymetrix
Chip type: CytoScanHD_Array
Algorithm parameters: {rescaleBy: chr "all", targetAvg: num 2200,
subsetToAvg: int [1:6538333] 1 2 3 4 5 6 7 8 11 12 ..., mergeShifts: logi
TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$
alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num
2, ..$ Q: num 98}
Output path: probeData/CNV,ACC,ra,-XY/CytoScanHD_Array
Is done: FALSE
> print(csC)
Error in print(csC) : object 'csC' not found
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.light_3.8.0 aroma.affymetrix_3.1.0 aroma.core_3.1.1
R.devices_2.15.1 R.filesets_2.11.0 R.utils_2.5.0
[7] R.oo_1.21.0affxparser_1.50.0 R.methodsS3_1.7.1
loaded via a namespace (and not attached):
[1] matrixStats_0.52.2 codetools_0.2-15 listenv_0.6.0 future_1.6.2
digest_0.6.12 R.huge_0.9.0 PSCBS_0.63.0
[8] tools_3.4.2R.cache_0.12.0 parallel_3.4.2
compiler_3.4.2 base64enc_0.1-3aroma.apd_0.6.0R.rsp_0.41.0
[15] globals_0.10.3 DNAcopy_1.52.0
> traceback()
No traceback available
On Wednesday, January 13, 2016 at 11:05:11 PM UTC+5, Henrik Bengtsson wrote:
>
> On Sun, Jan 10, 2016 at 11:36 PM, > wrote:
> >
> > Hi dear professor Henrik Bengtsson,
> >
> > When I was declaring the raw data set of CytoScan HD Array with
> aroma.affymetrix, I'm encountering the following errors:
> >
> > "Error: object 'csC' not found."
>
> It seems like you didn't run the command before. Make sure each
> object is actually created in every step by printing it, e.g.
> print(cdf), et
Re: [aroma.affymetrix] Error: object 'csC' not found.
Still the same; you're not calling csC <- process(acc, verbose=verbose) -- -- 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/d/optout.
Re: [aroma.affymetrix] Error: object 'csC' not found.
hello,have you solved your problem? I met the same error
在 2017年11月14日星期二 UTC+8上午8:29:07，ali jan写道：
>
> I tried your suggestion but it is still not working:
>
> > log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> > # Don't display too many decimals.
> > options(digits=4)
> >
> > cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
> > print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/CytoScanHD_Array
> Filename: CytoScanHD_Array.cdf
> File size: 612.27 MiB (642007896 bytes)
> Chip type: CytoScanHD_Array
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 2822125
> Cells per unit: 2.44
> Number of QC units: 4
> >
> > gi <- getGenomeInformation(cdf)
> > print(gi)
> UgpGenomeInformation:
> Name: CytoScanHD_Array
> Tags: na32,hg19,HB2008
> Full name: CytoScanHD_Array,na32,hg19,HB2008
> Pathname:
> annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB2008.ugp
> File size: 13.46 MiB (14111425 bytes)
> Chip type: CytoScanHD_Array
> >
> > si <- getSnpInformation(cdf)
> > print(si)
> UflSnpInformation:
> Name: CytoScanHD_Array
> Tags: na32,hg19,HB2008
> Full name: CytoScanHD_Array,na32,hg19,HB2008
> Pathname:
> annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,na32,hg19,HB2008.ufl
> File size: 5.38 MiB (5645047 bytes)
> Chip type: CytoScanHD_Array
> Number of enzymes: 1
> >
> > acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> > print(acs)
> AromaCellSequenceFile:
> Name: CytoScanHD_Array
> Tags: HB20111008
> Full name: CytoScanHD_Array,HB20111008
> Pathname:
> annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
> File size: 170.92 MiB (179217487 bytes)
> Number of data rows: 6892960
> File format: v1
> Dimensions: 6892960x26
> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw
> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> Footer: 2008 21:44:22
> PSTAffymetrixCytoScanHD_ArrayCytoScanHD_Array.probe_tab409176930beaaa56413608b3f9d9d464a07cddcaeHenrik
>
> Bengtssonhenrik.bengts...@aroma-project.org
>
> Chip type: CytoScanHD_Array
> Platform: Affymetrix
> >
> > csR <- AffymetrixCelSet$byName("CNV", cdf=cdf)
> > print(csR)
> AffymetrixCelSet:
> Name: CNV
> Tags:
> Path: rawData/CNV/CytoScanHD_Array
> Platform: Affymetrix
> Chip type: CytoScanHD_Array
> Number of arrays: 460
> Names: GSM1317174_H050150N-CytoScanHD_515-H050150N,
> GSM1317175_H050150T-CytoScanHD_516-H050150T,
> GSM1317176_H050154N-CytoScanHD_521-H050154N, ...,
> GSM1317635_H112971T-CytoScanHD_831-H112971T [460]
> Time period: 2012-03-12 16:49:41 -- 2012-04-05 08:47:43
> Total file size: 29.55 GiB
> >
> > cs <- csR
> > par(mar=c(4,4,1,1)+0.1)
> > plotDensity(cs, lwd=2, ylim=c(0,0.40))
>
> > acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
> > print(acc)
> AllelicCrosstalkCalibration:
> Data set: CNV
> Input tags:
> User tags: *
> Asterisk ('*') tags: ACC,ra,-XY
> Output tags: ACC,ra,-XY
> Number of files: 460 (29.55 GiB)
> Platform: Affymetrix
> Chip type: CytoScanHD_Array
> Algorithm parameters: {rescaleBy: chr "all", targetAvg: num 2200,
> subsetToAvg: int [1:6538333] 1 2 3 4 5 6 7 8 11 12 ..., mergeShifts: logi
> TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$
> alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num
> 2, ..$ Q: num 98}
> Output path: probeData/CNV,ACC,ra,-XY/CytoScanHD_Array
> Is done: FALSE
> > print(csC)
> Error in print(csC) : object 'csC' not found
> > sessionInfo()
> R version 3.4.2 (2017-09-28)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows >= 8 x64 (build 9200)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.light_3.8.0 aroma.affymetrix_3.1.0 aroma.core_3.1.1
> R.devices_2.15.1 R.filesets_2.11.0 R.utils_2.5.0
> [7] R.oo_1.21.0affxparser_1.50.0 R.methodsS3_1.7.1
>
> loaded via a namespace (and not attached):
> [1] matrixStats_0.52.2 codetools_0.2-15 listenv_0.6.0 future_1.6.2
> digest_0.6.12 R.huge_0.9.0 PSCBS_0.63.0
> [8] tools_3.4.2R.cache_0.12.0 parallel_3.4.2
> compiler_3.4.2 base64enc_0.1-3aroma.apd_0.6.0R.rsp_0.41.0
> [15] globals_0.10.3 DNAcopy_1.52.0
> > traceback()
> No traceback available
>
> On Wednesday, January 13, 2016 at 11:05:11 PM UTC+5, Henrik Bengtsson
> wrote:
>>
>> On Sun, Jan 10, 2016 at 11:36 PM, wrote:
Re: [aroma.affymetrix] Error: object 'csC' not found.
hello , i called the csC <- process(acc, verbose=verbose) and them print(csC), it still met Error: object 'csC' not found. 在 2017年11月24日星期五 UTC+8上午7:41:23，Henrik Bengtsson写道： > > Still the same; you're not calling > > csC <- process(acc, verbose=verbose) > -- -- 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/d/optout.
Re: [aroma.affymetrix] Error: object 'csC' not found.
If you called csC <- process(acc, verbose=verbose) and csC is not found, then there was an error during that call that you must pay attention to. /Henrik PS. Are you a single person reporting via three different email addresses, or are you two (three?) different people having the same problem? On Friday, November 24, 2017 at 12:18:31 PM UTC-8, 321bi...@gmail.com wrote: > > hello , i called the csC <- process(acc, verbose=verbose) and them > print(csC), it still met Error: object 'csC' not found. > 在 2017年11月24日星期五 UTC+8上午7:41:23，Henrik Bengtsson写道： >> >> Still the same; you're not calling >> >> csC <- process(acc, verbose=verbose) >> > -- -- 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/d/optout.
Re: [aroma.affymetrix] Error: object 'csC' not found.
On Sun, Jan 10, 2016 at 11:36 PM, wrote:
>
> Hi dear professor Henrik Bengtsson,
>
> When I was declaring the raw data set of CytoScan HD Array with
> aroma.affymetrix, I'm encountering the following errors:
>
> "Error: object 'csC' not found."
It seems like you didn't run the command before. Make sure each
object is actually created in every step by printing it, e.g.
print(cdf), etc. That should help you narrow down where your problem
is.
/Henrik
>
> I have searched the forum, unfortunately, I can't solve this problem.
>
> Could you give me some suggestions and help me solve it ?
>
> The following are the R code of mine:
>
> > setwd("G:/")
>
> >library("aroma.affymetrix")
>
> >log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>
> >options(digits=4)
>
> >cdf <- AffymetrixCdfFile$byChipType("CytoScanHD_Array")
>
> >gi <- getGenomeInformation(cdf)
>
> >si <- getSnpInformation(cdf)
>
> >acs <- AromaCellSequenceFile$byChipType(getChipType(cdf))
>
> >csR <- AffymetrixCelSet$byName("CytoScanHD_Array", cdf=cdf)
>
> >acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2")
>
> >csC <- process(acc, verbose=verbose)
>
> > print(csC)
>
> > sessionInfo()
> R version 3.2.2 (2015-08-14)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
>
> 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_2.4.0 aroma.affymetrix_2.14.0 affxparser_1.42.0
> [4] aroma.core_3.0.0R.devices_2.13.2R.filesets_2.10.0
> [7] R.utils_2.2.0 R.oo_1.19.0 R.methodsS3_1.7.0
>
> loaded via a namespace (and not attached):
>
> [1] matrixStats_0.50.1 codetools_0.2-14 listenv_0.6.0 future_0.10.0
> [5] digest_0.6.8 R.huge_0.9.0 PSCBS_0.60.0 tools_3.2.2
> [9] R.cache_0.12.0 parallel_3.2.2 base64enc_0.1-3aroma.apd_0.6.0
> [13] R.rsp_0.21.0 globals_0.6.0 DNAcopy_1.42.0
>
> CEL format raw data are locate in
> "G:/rawData/CytoScanHD_Array/CytoScanHD_Array"
>
> Looking forward your replay. Thank you very much.
>
>
>
>
>
>
>
>
> --
> --
> 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/d/optout.
--
--
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/d/optout.
