Respected Dr Bengtsson,
Thank you for your help. Sorry for not providing the sessionInfo() last
time. I am using aroma.affymetrix v 1.8.0. It solved that error but I am
facing a new error this time. The sessionInfo and the outputs are as
follows:
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
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_1.8.0 aroma.apd_0.1.7 affxparser_1.22.0
[4] R.huge_0.2.0 aroma.core_1.8.0 aroma.light_1.18.2
[7] matrixStats_0.2.2 R.rsp_0.4.0 R.filesets_0.9.1
[10] digest_0.4.2 R.cache_0.3.0 R.utils_1.5.8
[13] R.oo_1.7.4 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] affy_1.28.0 affyio_1.18.0 Biobase_2.10.0
[4] Biostrings_2.18.0 gcrma_2.22.0 IRanges_1.8.2
[7] preprocessCore_1.12.0 splines_2.12.0 tools_2.12.0
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("aroma.affymetrix")
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("aroma.cn")
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
> dataSet <- "Exon Data"
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
> print(cdf)
> acs<-getAromaCellSequenceFile(cdf)
> print(acs)
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
> 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: 4 (251.42MB)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
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/HuEx-1_0-st-v2
Is done: FALSE
RAM: 0.00MB
> csB <- process(bc, verbose=verbose)
20101203 14:04:42|Background correcting data set...
20101203 14:04:42| Computing probe affinities (independent of data)...
20101203 14:04:42| Computing GCRMA probe affinities...
20101203 14:04:42| Chip type: HuEx-1_0-st-v2
20101203 14:04:42| Number of units: 297051
20101203 14:04:43| Cached results found.
20101203 14:04:43| Computing GCRMA probe affinities...done
20101203 14:04:43| RAM: 50.00MB
20101203 14:04:43| Computing probe affinities (independent of data)...done
20101203 14:04:43| Background correcting data set...
20101203 14:04:44| Already background corrected for "optical" effects
20101203 14:04:44| Background correcting data set...done
20101203 14:04:44| Estimating specific binding parameters (data
dependent)...
20101203 14:04:44| Extracting PM indices...
20101203 14:04:44| Reading cell indices from CDF file...
20101203 14:04:44| Pathname:
annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
20101203 14:04:44| Units:
NULL
20101203 14:04:44| lapplyInChunks()...
20101203 14:04:44| Number of elements per chunk: 1e+05
20101203 14:04:44| Chunk #1 of 3...
20101203 14:04:44| Elements:
int [1:100000] 1 2 3 4 5 6 7 8 9 10 ...
20101203 14:04:44| Querying CDF file...
20101203 14:05:08| Querying CDF file...done
20101203 14:05:08| Restructuring...
20101203 14:05:08| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 5354837 143.0 6193578 165.4 5373715 143.5
Vcells 13471411 102.8 20149605 153.8 13475095 102.9
20101203 14:05:09| Chunk #1 of 3...done
20101203 14:05:09| Chunk #2 of 3...
20101203 14:05:09| Elements:
int [1:100000] 100001 100002 100003 100004 100005 100006 100007
100008 100009 100010 ...
20101203 14:05:09| Querying CDF file...
20101203 14:05:15| Querying CDF file...done
20101203 14:05:15| Restructuring...
20101203 14:05:15| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1491395 39.9 4954862 132.4 6193578 165.4
Vcells 10685280 81.6 20149605 153.8 17357812 132.5
20101203 14:05:16| Chunk #2 of 3...done
20101203 14:05:16| Chunk #3 of 3...
20101203 14:05:16| Elements:
int [1:97051] 200001 200002 200003 200004 200005 200006 200007 200008
200009 200010 ...
20101203 14:05:16| Querying CDF file...
20101203 14:05:20| Querying CDF file...done
20101203 14:05:21| Restructuring...
20101203 14:05:21| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1471326 39.3 4954862 132.4 6193578 165.4
Vcells 10882001 83.1 20149605 153.8 17357812 132.5
20101203 14:05:21| Chunk #3 of 3...done
20101203 14:05:21| lapplyInChunks()...done
20101203 14:05:21| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 336599 9.0 3963889 105.9 6193578 165.4
Vcells 9592574 73.2 20149605 153.8 17357812 132.5
20101203 14:05:21| readUnits.AffymetrixCdfFile(): Updating cache
20101203 14:05:49| Extracting PM indices...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 336674 9.0 2849399 76.1 6193578 165.4
Vcells 7232054 55.2 23577885 179.9 23043337 175.9
20101203 14:05:49| Extracting 25000 random PM intensities across CEL set...
20101203 14:05:49| Array #1 of 4...
20101203 14:05:50| Array #1 of 4...done
20101203 14:05:50| Array #2 of 4...
20101203 14:05:50| Array #2 of 4...done
20101203 14:05:50| Array #3 of 4...
20101203 14:05:50| Array #3 of 4...done
20101203 14:05:50| Array #4 of 4...
20101203 14:05:50| Array #4 of 4...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 337074 9.1 2279519 60.9 6193578 165.4
Vcells 7257179 55.4 23577885 179.9 23043337 175.9
20101203 14:05:50| Extracting 25000 random PM intensities across CEL
set...done
20101203 14:05:50| Extracting probe affinities and fitting linear model...
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 337074 9.1 1823615 48.7 6193578 165.4
Vcells 7269671 55.5 23577885 179.9 23043337 175.9
20101203 14:05:51| Fitting the GCRMA background linear model...
num [1:25000] 6.13 10.17 5.73 7.87 10.87 ...
num [1:25000] 0.097 0.771 0.181 0.443 1.88 ...
Call:
lm(formula = pm.random2 ~ aff)
Coefficients:
(Intercept) aff
7.104 0.597
20101203 14:05:51| Fitting the GCRMA background linear model...done
20101203 14:05:51| Extracting probe affinities and fitting linear
model...done
20101203 14:05:51| parametersGsb:
(Intercept) aff
7.1042892 0.5969684
20101203 14:05:51| Estimating specific binding parameters (data
dependent)...done
20101203 14:05:51| Adjusting 4 arrays...
20101203 14:05:51| Array #1 of 4...
AffymetrixCelFile:
Name: 10 ZEB1_(HuEx-1_0-st-v2)
Tags:
Full name: 10 ZEB1_(HuEx-1_0-st-v2)
Pathname: probeData/Exon Data,OBC/HuEx-1_0-st-v2/10
ZEB1_(HuEx-1_0-st-v2).CEL
File size: 62.50 MB (65536714 bytes)
RAM: 0.00 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
Timestamp: 2010-12-03 13:43:43
20101203 14:05:51| Retrieving PM and MM signals and affinities...
20101203 14:06:26| Number of PM probes: 5270074
20101203 14:06:26| Number of MM probes: 0
20101203 14:06:42| PM signals:
num [1:5270074] 237 480 120 482 421 ...
20101203 14:06:42| MM signals:
num(0)
20101203 14:06:43| PM affinities:
num [1:5270074] -0.585 -1.687 -1.664 -0.569 1.626 ...
20101203 14:06:43| MM affinities:
num(0)
20101203 14:06:43| Retrieving PM and MM signals and affinities...done
20101203 14:06:43| Estimating non-specific binding parameters...
20101203 14:06:43| Model type/flavor: affinities
20101203 14:06:43| Affinity-based GCRMA model background adjustment...
20101203 14:06:43| Using mismatch probes (MMs) as negative controls
20101203 14:06:43| Dropping perfect-match probes (PMs) with missing
signals or missing affinities...
20101203 14:06:43| Number of finite PMs: 5270074 out of 5270074
(100.0%)
20101203 14:06:43| Number of finite PM affinities: 5270074 out of
5270074 (100.0%)
20101203 14:06:44| Number of PMs kept: 5270074 out of 5270074 (100.0%)
20101203 14:06:45| Dropping perfect-match probes (PMs) with missing
signals or missing affinities...done
20101203 14:06:45| Dropping negative controls with missing signals or
missing affinities...
20101203 14:06:45| Number of finite negative controls: 0 out of 0
(NaN%)
20101203 14:06:45| Number of finite negative-control affinities: 0 out
of 0 (NaN%)
20101203 14:06:45| Number of negative controls kept: 0 out of 0 (NaN%)
20101203 14:06:45| Dropping negative controls with missing signals or
missing affinities...done
20101203 14:06:45| Number of PMs: 5270074
20101203 14:06:45| Number of negative controls: 0
Error in if (from == to) rep.int(from, length.out) else as.vector(c(from,
:
missing value where TRUE/FALSE needed
20101203 14:06:49| Array #1 of 4...done
20101203 14:06:49| Adjusting 4 arrays...done
20101203 14:06:49|Background correcting data set...done
Please help me in this regard. Also The passing of cdf and ptf arguments in
process() is just the trial-error I was trying. I am really sorry for that
and should have given you the code I have.
Yours Faithfully,
Prithish Banerjee,
Graduate Research Assistant,
Department of Statistics,
West Virginia University.
On Fri, Dec 3, 2010 at 2:50 AM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> Hi.
>
> On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee
> <prithish.baner...@gmail.com> wrote:
> > Respected Dr Bengtsson,
> > I have the following codes and outputs:
> >> source("http://aroma-project.org/hbLite.R";);
> >> hbInstall("aroma.affymetrix")
>
> I'll assume that you've run this recently so that you have
> aroma.affymetrix v1.8.0 installed, because then you can do what I
> explain next. FYI, whenever you get an error, please report what
> sessionInfo() gives so we can be sure you're up-to-date.
>
> Go to the HuEx-1_0-st-v2 chip type page:
>
> http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/
>
> and download the Aroma Cell Sequence (ACS) file. Place it in
> annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is). Don't
> forget to gunzip.
>
> You can drop/move/leave the probe-tab file; it won't be needed anymore.
>
> The following script should do:
>
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
> dataSet <- "Exon Data";
> chipType <- "HuEx-1_0-st-v2";
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP");
> print(cdf);
>
> # Assert that the ACS file is available (not really needed to be done)
> acs <- getAromaCellSequenceFile(cdf);
> print(acs);
>
> # GCRMA background correction
> bc <- GcRmaBackgroundCorrection(csR, type="affinities");
> print(bc);
> csB <- process(bc, verbose=verbose);
> print(csB);
>
> Finally, I've noticed that you've tried to pass arguments 'cdf' and
> 'ptf' to process(), i.e.
>
> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose);
>
> That is not correct. Was that suggested to you anywhere, or is it
> just part of your trial-and-error?
>
> Let me know if this solves your problem
>
> /Henrik
>
> >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
> >> dataSet <- "Exon Data"
> >> chipType <- "HuEx-1_0-st-v2"
> >> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP")
> >> print(cdf)
> > AffymetrixCdfFile:
> > Path: annotationData/chipTypes/HuEx-1_0-st-v2
> > Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf
> > Filesize: 203.31MB
> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> > RAM: 0.00MB
> > File format: v4 (binary; XDA)
> > Dimension: 2560x2560
> > Number of cells: 6553600
> > Number of units: 297051
> > Cells per unit: 22.06
> > Number of QC units: 1
> >> ptf <- AffymetrixProbeTabFile$byChipType(chipType);
> >> print(ptf)
> > AffymetrixProbeTabFile:
> > Name: HuEx-1_0-st-v2
> > Tags:
> > Full name: HuEx-1_0-st-v2
> > Pathname:
> annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
> > File size: 527.80 MB (553438704 bytes)
> > RAM: 0.01 MB
> > Number of data rows: NA
> > Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
> 'assembly',
> > 'seqname', 'start', 'stop', 'strand', 'probeSequence',
> 'targetStrandedness',
> > 'category'
> > Number of text lines: NA
> > AffymetrixCdfFile:
> > Path: annotationData/chipTypes/HuEx-1_0-st-v2
> > Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
> > Filesize: 38.25MB
> > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
> > RAM: 0.00MB
> > File format: v4 (binary; XDA)
> > Dimension: 2560x2560
> > Number of cells: 6553600
> > Number of units: 18708
> > Cells per unit: 350.31
> > Number of QC units: 1
> >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf)
> >> print(csR)
> > AffymetrixCelSet:
> > Name: Exon Data
> > Tags:
> > Path: rawData/Exon Data/HuEx-1_0-st-v2
> > Platform: Affymetrix
> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> > Number of arrays: 17
> > Names: 10_5N, 11_6T, ..., 9_5T
> > Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40
> > Total file size: 1081.22MB
> > RAM: 0.02MB
> >> 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: 17 (1081.22MB)
> > Platform: Affymetrix
> > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP
> > 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/HuEx-1_0-st-v2
> > Is done: FALSE
> > RAM: 0.00MB
> >> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose)
> > 20101202 14:46:02|Background correcting data set...
> > 20101202 14:46:02| Computing probe affinities (independent of data)...
> > 20101202 14:46:03| Computing GCRMA probe affinities...
> > 20101202 14:46:03| Chip type: HuEx-1_0-st-v2
> > 20101202 14:46:03| Number of units: 297051
> > 20101202 14:46:03| Locating the cell sequence annotation data file...
> > 20101202 14:46:03| Locating the cell sequence annotation data
> file...done
> > 20101202 14:46:03| Computing GCRMA probe affinities...done
> > 20101202 14:46:03| Computing GCRMA probe affinities...
> > 20101202 14:46:03| Number of units: 297051
> > 20101202 14:46:03| Identify PMs and MMs among the CDF cell indices...
> > logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ...
> > Mode TRUE NA's
> > logical 5270074 0
> > 20101202 14:46:52| MMs are defined as non-PMs
> > 20101202 14:46:52| Number of PMs: 5270074
> > 20101202 14:46:52| Number of MMs: 0
> > 20101202 14:46:52| Identify PMs and MMs among the CDF cell
> indices...done
> > 20101202 14:46:52| Reading probe-sequence data...
> > 20101202 14:46:52| Retrieving probe-sequence data...
> > 20101202 14:46:52| Chip type (full):
> HuEx-1_0-st-v2,fullR3,A20071112,EP
> > 20101202 14:46:52| Locating probe-tab file...
> > 20101202 14:46:52| Chip type: HuEx-1_0-st-v2
> > AffymetrixProbeTabFile:
> > Name: HuEx-1_0-st-v2
> > Tags:
> > Full name: HuEx-1_0-st-v2
> > Pathname:
> > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
> > File size: 527.80 MB (553438704 bytes)
> > RAM: 0.01 MB
> > Number of data rows: NA
> > Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos',
> > 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence',
> > 'targetStrandedness', 'category'
> > Number of text lines: NA
> > AffymetrixCdfFile:
> > Path: annotationData/chipTypes/HuEx-1_0-st-v2
> > Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
> > Filesize: 38.25MB
> > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
> > RAM: 0.00MB
> > File format: v4 (binary; XDA)
> > Dimension: 2560x2560
> > Number of cells: 6553600
> > Number of units: 18708
> > Cells per unit: 350.31
> > Number of QC units: 1
> > 20101202 14:46:52| Locating probe-tab file...done
> > 20101202 14:46:52| Validating probe-tab file against CDF...
> > 20101202 14:46:52| Number of records read: 1
> > 20101202 14:46:52| Data read:
> > 'data.frame': 1 obs. of 1 variable:
> > $ probeSetID: chr "2315101"
> > - attr(*, "fileHeader")=List of 6
> > ..$ comments: NULL
> > ..$ sep : chr "\t"
> > ..$ quote : chr "\""
> > ..$ skip : num 0
> > ..$ topRows :List of 10
> > .. ..$ : chr "Probe ID" "Probe Set ID" "probe x" "probe y" ...
> > .. ..$ : chr "494998" "2315101" "917" "193" ...
> > .. ..$ : chr "1734213" "2315101" "1092" "677" ...
> > .. ..$ : chr "4767517" "2315101" "796" "1862" ...
> > .. ..$ : chr "4286427" "2315101" "986" "1674" ...
> > .. ..$ : chr "5760145" "2315102" "144" "2250" ...
> > .. ..$ : chr "671410" "2315102" "689" "262" ...
> > .. ..$ : chr "4275780" "2315102" "579" "1670" ...
> > .. ..$ : chr "4293462" "2315102" "341" "1677" ...
> > .. ..$ : chr "5388" "2315103" "267" "2" ...
> > ..$ columns : chr "Probe ID" "Probe Set ID" "probe x" "probe y"
> ...
> > 20101202 14:46:52| Unit name:
> > chr "2315101"
> > 20101202 14:46:55| Unit index: NA
> > Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` =
> > <environment>, :
> >
> > [2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit
> name
> > '2315101':
> annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab
> > at throw(Exception(...))
> > at throw.default("Failed to identify CDF unit with unit name '", unitNa
> > at throw("Failed to identify CDF unit with unit name '", unitName, "':
> > 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/HuEx-1_0-st-v2",
> > at do.call("bgAdjustGcrma", args = args)
> > at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose
> > at process(bc, cdf = cdf, ptf = ptf, verbose = verbose)
> > 20101202 14:46:55| Validating probe-tab file against CDF...done
> > 20101202 14:46:55| Retrieving probe-sequence data...done
> > 20101202 14:46:55| Reading probe-sequence data...done
> > 20101202 14:46:55| Computing GCRMA probe affinities...done
> > 20101202 14:46:55| Computing probe affinities (independent of
> data)...done
> > 20101202 14:46:55|Background correcting data set...done
> >
> > Could you please tell me how to rectify the error?
> > Thank you.
> > Prithish Banerjee,
> > Graduate Research Assistant,
> > Department of Statistics,
> > West Virginia University.
> >
> > --
> > 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/
