Dear all,
I just start learning aroma.affymetrix package for Affy SNP6.0
analysis. I downloaded ugp,ufl,acs file from the link
http://www.aroma-project.org/chipTypes/GenomeWideSNP_6, followed the
example code, but I got the following warnings. I can't move to the
following steps. Would you please let me know what the problem is?
Thanks a lot,
Qian
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6",tags="Full");
> print(cdf);
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
> gi <- getGenomeInformation(cdf)
Warning messages:
1: In readBin(con = con, what = integer(), size = 4, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
5: In readBin(con = con, what = integer(), size = 4, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
6: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
7: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
8: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
> print(gi);
UgpGenomeInformation:
Name: GenomeWideSNP_6
Tags: Full,na31,hg19,HB20110328
Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
File size: 8.97 MB (9407867 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Warning messages:
1: In readBin(con = con, what = integer(), size = 4, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
5: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
> si <- getSnpInformation(cdf)
Warning messages:
1: In readBin(con = con, what = integer(), size = 4, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
> print(si)
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na31,hg19,HB20110328
Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
File size: 7.18 MB (7526452 bytes)
RAM: 0.00 MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
Warning messages:
1: In readBin(con = con, what = integer(), size = 4, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
2: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
3: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
4: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
5: In readBin(con = con, what = integer(), size = 4, n = n, signed =
FALSE, :
'signed = FALSE' is only valid for integers of sizes 1 and 2
> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
> print(acs)
AromaCellSequenceFile:
Name: GenomeWideSNP_6
Tags: HB20080710
Full name: GenomeWideSNP_6,HB20080710
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,HB20080710.acs
File size: 170.92 MB (179217531 bytes)
RAM: 0.00 MB
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: <createdOn>20080710 22:47:02 PDT</
createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</
chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</
filename><filesize>341479928</
filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></
srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</
filename><filesize>96968290</
filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></
srcFile2>
Chip type: GenomeWideSNP_6
Platform: Affymetrix
There were 19 warnings (use warnings() to see them)
> csR <- AffymetrixCelSet$byName("GenomeWideSNP_6,dataSet1", cdf=cdf)
Error in list(`AffymetrixCelSet$byName("GenomeWideSNP_6,dataSet1", cdf
= cdf)` = <environment>, :
[2011-10-14 16:49:32] Exception: Cannot create AffymetrixCelSet. No
such directory: GenomeWideSNP_6,dataSet1/GenomeWideSNP_6
at throw(Exception(...))
at throw.default("Cannot create ", class(static)[1], ". No such
directory: ", path)
at throw("Cannot create ", class(static)[1], ". No such directory:
", path)
at method(static, ...)
at AffymetrixCelSet$byName("GenomeWideSNP_6,dataSet1", cdf = cdf)
> sessionInfo()
R version 2.13.2 (2011-09-30)
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
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods
base
other attached packages:
[1] aroma.affymetrix_2.2.0 affxparser_1.24.0
aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.2.0
aroma.light_1.21.2
[7] matrixStats_0.2.2 R.rsp_0.6.2
R.cache_0.5.2 R.filesets_1.1.0 digest_0.5.1
R.utils_1.8.2
[13] R.oo_1.8.2 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.13.2
--
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traceback(), and 3) to post a complete code example.
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