Error when Creating binary data files containing copy number estimates (Agilent HG-CGH-244A)

[sean nj]

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
>

 

 

[sean nj]

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'

>

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
>

 

 

--
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[Pierre Neuvial]

Hi,

On Wed, May 16, 2012 at 9:05 PM, sean nj <njs...@gmail.com> 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

[sean nj]

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

[sean nj]

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

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>
>
> --
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>
>
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[sean nj]

Hi Pierre,

 

I think I know what units for now. I used units <- c(1:235834) and it worked.

 

Thanks,

 

Ying

 

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