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)
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: bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon
Data,GRBC/MoEx-1_0-st-v1",
verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
NULL,
type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
gsbParameters = NULL, .deprecated = FALSE)
4: bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
verbose = TRUE, overwrite = FALSE, subsetToUpdate = NULL,
typesToUpdate = "pm", indicesNegativeControl = NULL, affinities =
NULL,
type = "affinities", opticalAdjust = TRUE, gsbAdjust = TRUE,
gsbParameters = NULL, .deprecated = FALSE)
3: do.call("bgAdjustGcrma", args = args)
2: process.GcRmaBackgroundCorrection(bc, verbose = verbose)
1: process(bc, verbose = verbose)
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-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 base
other attached packages:
[1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0
[4] R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1
[7] matrixStats_0.2.1 R.rsp_0.4.0 R.filesets_0.9.0
[10] digest_0.4.2 R.cache_0.3.0 R.utils_1.5.2
[13] R.oo_1.7.4 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.11.1
The working directory is desktop and the path for the cdf file and the raw
data is as follows:
/Users/prithish/Desktop/annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
( I have several other cdf files
like
MoEx-1_0-st-v1,extendedR1,A20080718,MR.cdf/MoEx-1_0-st-v1,fullR1,A20080718,MR.cdf
and MoEx-1_0-st-v1.cdf in the same directory.)
/Users/prithish/Desktop/rawData/Exon Data/MoEx-1_0-st-v1/
DK Litter D15 P1_(MoEx-1_0-st-v1).CEL
DK Litter D15 P2_(MoEx-1_0-st-v1).CEL
DK Litter D15 P3 #2_(MoEx-1_0-st-v1).CEL
DK Litter D15 P3_(MoEx-1_0-st-v1).CEL
DK Litter D15 P6_(MoEx-1_0-st-v1).CEL
DK Litter D15 P14_(MoEx-1_0-st-v1).CEL
Moreover I am following the thread and implementing the code you suggested
there but it is not working with my dataset. Please help.
Thank you,
Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.
On Sun, Sep 26, 2010 at 4:23 PM, Henrik Bengtsson <h...@aroma-project.org>wrote:
> Hi,
>
> first of all, for this chip type you need to specify:
>
> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
>
> Moreover, you cannot use the custom CDF in the
> GcRmaBackgroundCorrection step, and have to do the follow workaround
> illustrated in the below example:
>
>
> library("aroma.affymetrix");
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
> dataSet <- "Affymetrix-Tissues";
> chipType <- "MoEx-1_0-st-v1";
>
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Setup data set
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR");
> print(cdf);
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
> print(csR);
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # gcRMA-style background correction
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Currently, you must use the standard CDF file.
> cdf <- getCdf(csR);
> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
> setCdf(csR, cdfS);
> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
> print(bc);
> csB <- process(bc, verbose=verbose);
> print(csB);
> # Now, use the custom CDF in what follows
> setCdf(csB, cdf);
> print(csB);
>
> Yes, those last steps are rather confusing - we're working on updating
> the code so you don't have to do that yourself.
>
> FYI, the above solution/workaround was resolved in thread 'GCRMA
> normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
> http://goo.gl/cniq.
>
> Hope this helps
>
> /Henrik
>
> On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
> <prithish.baner...@gmail.com> wrote:
> > Hi All,
> > I am trying to normalize a mouse exon array dataset using GCRMA
> > normalization technique. I have exactly followed all the necessary steps
> for
> > storing the dataset and the cdf file. the code and the output I am using
> 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$getVerbose(-10, timestamp=TRUE);
> >
> > dataSet <- "Exon Data" [the path in the working directory is rawData/Exon
> > Data/MoEx-1_0-st-v1/*.CEL files]
> >
> > chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
> >
> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
> >
> > cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
> > [converted to binary using convertCdf command]
> >
> > 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)
> >
> > 20100923 13:24:12|Background correcting data set...
> >
> > 20100923 13:24:12| Computing probe affinities...
> >
> > 20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units...
> >
> > 20100923 13:24:12| 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
> >
> > 20100923 13:25:57| MMs are defined as non-PMs
> >
> > 20100923 13:25:57| Number of PMs: 4931683
> >
> > 20100923 13:25:57| Number of MMs: 334476
> >
> > 20100923 13:25:57| Identify PMs and MMs among the CDF cell
> indices...done
> >
> > 20100923 13:25:57| Reading probe-sequence data...
> >
> > 20100923 13:25:57| Retrieving probe-sequence data...
> >
> > 20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1
> >
> > 20100923 13:25:57| Locating probe-tab file...
> >
> > 20100923 13:25:57| Chip type: MoEx-1_0-st-v1
> >
> > Error in list(`process(bc, verbose = verbose)` = <environment>,
> > `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` =
> <environment>,
> > :
> >
> >
> >
> > [2010-09-23 13:25:57] 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(
> >
> > 20100923 13:25:57| Locating probe-tab file...done
> >
> > 20100923 13:25:57| Retrieving probe-sequence data...done
> >
> > 20100923 13:25:57| Reading probe-sequence data...done
> >
> > 20100923 13:25:57| Computing GCRMA probe affinities for 1257006
> > units...done
> >
> > 20100923 13:25:57| Computing probe affinities...done
> >
> > 20100923 13:25:57|Background correcting data set...done
> >
> > Could anyone please enlighten me with the type of the error? I will be
> > highly obliged if anyone please help me with this problem.
> >
> > Thank you.
> >
> > Prithish Banerjee.
> >
> >
> >
> > --
> > 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/
>
--
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/
