Hi Pierre,
Sorry to bother you again.
I am following the Vignette: Creating binary data files containing copy
number estimates (http://www.aroma-project.org/node/88) and trying to
create a UGP file. But I am confused with the codes listed:
units <- c(1,4,7);
ugp[units,1] <- 1;
ugp[units,2] <- c(554268, 736483, 757922);
I tried to find some information regarding ugp, but had no success. My
question is what the units <- c(1,4,7)for? What does 1, 4, and 7 mean?
I want to make a ugp file for Agilent UG-CGH-244A chip files I got from
TCGA-GBM data, which has 235834 probes. When I used units <- c(1,4,7),
> mydata <- read.delim(file.choose())
> mydata <- as.data.frame(mydata)
> str(mydata)
'data.frame': 235834 obs. of 12 variables:
$ unitName :
Factor w/ 235834 levels "A_14_P100000",..: 12409 103695 103696 41581 41582
41583 41584 41585 41586 41587 ...
$ unitCount :
int 1 2 3 4 5 6 7 8 9 10 ...
$ Gene_Symbol :
Factor w/ 16808 levels "","1-Dec","1-Mar",..: 1 1 1 1 1 1 1 1 1 1 ...
$ Description :
Factor w/ 16670 levels "","1-acylglycerol-3-phosphate O-acyltransferase 1
(lysophosphatidic acid acyltransferase, alpha)",..: 1 1 1 1 1 1 1 1 1 1 ...
$ Chromosome :
int 1 1 1 1 1 1 1 1 1 1 ...
$ chr_start :
int 604268 604287 689581 786483 792533 796956 807922 819590 834458 842413
...
$ chr_end :
int 604327 604346 689640 786542 792586 797005 807966 819649 834517 842458
...
$ Cytoband :
Factor w/ 259 levels "","hs|p11","hs|p11.1",..: 97 97 97 97 97 97 97 97 97
97 ...
$ Reporter..genbank..Comment.OMOSOMAL_LOCATION..Comment.ACCESSION_STRING.:
Factor w/ 235649 levels ":::","::NC_000001.8[000786483..000786542]:",..:
85381 85382 91604 2 3 4 101218 101217 87259 5 ...
$ Chr :
int 1 1 1 1 1 1 1 1 1 1 ...
$ Start_GRCH37 :
int 564405 564424 649718 746620 752670 757093 768059 779727 794595 802550
...
$ End_GRCH37 :
int 564464 564483 649777 746679 752723 757142 768103 779786 794654 802595
...
> units <- c(1,4,7)
> ugp[units,1] <- mydata$Chromosome
> ugp[units,2] <- mydata$chr_start
> print(ugp[units,])
chromosome position
1 1 604268
2 1 604287
3 1 689581
Here I only got 3 probes, instead of 235834.
> print(ugp[1:4,])
chromosome position
1 1 604268
2 NA NA
3 NA NA
4 1 604287
>
Here I am not sure where the NAs are from.
Any suggestion?
Thanks a lot for the help!
Ying
On Wednesday, May 16, 2012 4:19:31 PM UTC-4, sean nj wrote:
> Hi Pierre,
>
> I figured out what's wrong. I did not set the object unitNames.
>
> After I ran
>
> > unitNames <- getUnitNames(unf)
> > units <- indexOf(unf,names=unitNames)
>
> it works now.
>
> Thanks,
>
>
> Ying
>
>
>
>
> On Wed, May 16, 2012 at 3:44 PM, Pierre Neuvial
> <[email protected]>wrote:
>
>> Hi,
>>
>> On Wed, May 16, 2012 at 9:05 PM, sean nj <[email protected]> wrote:
>> >
>> > Hi,
>> >
>> > I did get rid of the error message when I ran :
>> >
>> > > unf <-
>> TextUnitNamesFile$byChipType(chipType)
>> >
>> > I got this done by loading the aroma.affymetrix package, in addition to
>> aroma.core.
>> >
>> > But now I got another error message when I followed Henrik's code at
>> http://aroma-project.org/node/88
>> >
>> > I was trying to creating data files containing log2 CN ratios.
>> Everything was fine until I ran
>> >
>> > > units <- indexOf(unf, unitNames)
>> > Error in indexOf.UnitNamesFile(unf, unitNames) :
>> > [2012-05-16 14:53:18] Exception: If specified, argument 'pattern' must
>> be a single string. Did you mean to use argument 'names'?
>> > at #02. indexOf.UnitNamesFile(unf, unitNames)
>> > - indexOf.UnitNamesFile() is in environment 'aroma.core'
>> > at #01. indexOf(unf, unitNames)
>> > - indexOf() is in environment 'R.filesets'
>> > >
>> >
>>
>> From the error message (pretty explicit) it looks like you should have
>> done
>>
>> units <- indexOf(unf, names=unitNames)
>>
>> instead of
>>
>> units <- indexOf(unf, unitNames)
>>
>> That's what you do below.
>>
>> Cheers,
>>
>> Pierre
>>
>> > The command ran successfully when I tried to get units for certain
>> probes
>> >
>> > > units <- indexOf(unf, names=c("A_16_P15025341","A_16_P00013121")
>> > + )
>> > > units
>> > [1] 1006 1019
>> > >
>> > I tried > ?indexOf.UnitNamesFile() and here is what I got:
>> >
>> > indexOf(this, pattern=NULL, names=NULL, ...)
>> >
>> > Arguments
>> >
>> > pattern A pattern to be used for identifying unit names of
>> interest. If NULL, no regular expression matching is done.
>> >
>> >
>> >
>> > names Names to be match exactly to the unit names.
>> >
>> > ... Not used.
>> >
>> >
>> > What did I do wrong?
>> >
>> > Thanks a lot for the help!
>> >
>> > Ying
>> >
>> > > sessionInfo()
>> > R version 2.15.0 (2012-03-30)
>> > Platform: x86_64-pc-mingw32/x64 (64-bit)
>> > locale:
>> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
>> States.1252
>> > [3] LC_MONETARY=English_United States.1252 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.affymetrix_2.5.0 affxparser_1.28.0
>> aroma.apd_0.2.2 R.huge_0.3.0
>> > [5] aroma.core_2.5.0 aroma.light_1.24.0
>> matrixStats_0.5.0 R.rsp_0.7.5
>> > [9] R.filesets_1.1.5 digest_0.5.2
>> R.cache_0.6.2 R.utils_1.12.1
>> > [13] R.oo_1.9.3 R.methodsS3_1.2.2
>> > loaded via a namespace (and not attached):
>> > [1] tools_2.15.0
>> > >
>> >
>> >
>> > On Tue, May 15, 2012 at 12:38 PM, sean nj <[email protected]> wrote:
>> >>
>> >> Hi guys,
>> >>
>> >> I was following the Vignette: Creating binary data files containing
>> copy number estimates and trying to work on agilent HG-CGH-244A chip. I
>> downloaded and unzipped the .gz of the
>> HG-CGH-244A,TCGA,HB20080512,unitNames.txt and
>> HG-CGH-244A,TCGA,HB20080512.ugp and put them in
>> H:\Aroma_Analysis\annotationData\chipTypes\HG-CGH-244A folder. Then I tried
>> to run the same code on the vignette and got the error right away (please
>> see end of this email). Did I do something wrong?
>> >>
>> >> I have one more question regarding "Creating data files containing
>> log2 CN ratios" with HG-CGH-244A chip. The data I have are level 2 files
>> from TCGA. There is one txt file for each sample (not the original .asb
>> file) and its format is like:
>> >>
>> >>
>> >> Hybridization REF MSK_00001_251469322729_S01_CGH-v4_91
>> >>
>> >> Composite Element REF normalizedLog2Ratio
>> >>
>> >> A_14_P112718 0.135431541355747
>> >>
>> >> A_16_P15000916 0.441719513563848
>> >>
>> >> A_16_P15001074 0.227252175271962
>> >>
>> >> A_16_P00000012 0.231158251618718
>> >>
>> >> A_16_P00000014 -0.0623833233443793
>> >>
>> >> .........................................................
>> >>
>> >> ..........................................................
>> >>
>> >> My first question is, does this kind data file work?
>> >>
>> >> My second question is, do I need to create a folder rawCnData as
>> mentioned in the vignette (Pathname:
>> rawCnData/MyDataSet,tagA,tagB/HG-CGH-244A/SampleA,tagA,tagB,log2ratio,total.asb)?
>>
>> I also have the rawData folder which holds affy snp6 and expression data.
>> >>
>> >>
>> >>
>> >> Thanks a lot for the help!
>> >>
>> >>
>> >>
>> >> Ying
>> >>
>> >> > library(aroma.core)
>> >> > chipType <- "HG-CGH-244A"
>> >> > unf <- TextUnitNamesFile$byChipType(chipType)
>> >> Error in method(static, ...) :
>> >> [2012-05-15 12:12:26] Exception: Failed to create TextUnitNamesFile
>> object. Could to locate an annotation data file for chip type 'HG-CGH-244A'
>> (without requiring any tags) and with filename extension 'names' (this may
>> not be the correct extension as it was guessed from the class name
>> 'TextUnitNamesFile').
>> >>
>> >> at #02. method(static, ...)
>> >> - method() is in environment 'aroma.core'
>> >> at #01. TextUnitNamesFile$byChipType(chipType)
>> >> - TextUnitNamesFile$byChipType() is local of the calling
>> function
>> >> > sessionInfo()
>> >> R version 2.15.0 (2012-03-30)
>> >> Platform: x86_64-pc-mingw32/x64 (64-bit)
>> >> locale:
>> >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
>> States.1252 LC_MONETARY=English_United States.1252 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.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.0
>> R.rsp_0.7.5 R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2
>> R.utils_1.12.1
>> >> [9] R.oo_1.9.3 R.methodsS3_1.2.2
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> 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 [email protected]
>> >> 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 [email protected]
>> > 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 [email protected]
>> 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 [email protected]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
