I'm having some trouble creating a CDF file from the PDInforBuilder
library for the "HuGene-1_0-st-v1". I want to use the latest "r4" pgf
and clf files, and the "r3" CEL file available from Affy does not have
the non-genomic probes. I attempted to follow the instructions at
http://www.aroma-project.org/node/41 but first off was getting an
error "Error in `[.data.frame`(probesets, , cols) : undefined columns
selected". When I looked at the vignette I noticed that the probeFile
was the probeset.csv and not probe.tab. I changed that and then the
next error was that the transFile was not of the correct class
"ScalarCharacter", and that the coreMPS file was not specified. I
fixed that and was able to make the package and install it. However,
when I create the CDF file using the PdInfo2Cdf script, the resulting
CEL file is much larger than I would expect (53,186 KB) and has 253002
units, as oppose to the 33252 that you get with the old version
http://www.aroma-project.org/node/30. Any idea what I did wrong?
I used the following code to create the package and install it to my library:
library(pdInfoBuilder)
baseDir <- "P:\\ANNOTATION\\AffyAnnotation\\Human\\HuGene-1_0-st-v1"
pgf <- mkScalar(list.files(baseDir, pattern = ".pgf", full.names = TRUE))
clf <- mkScalar(list.files(baseDir, pattern = ".clf", full.names = TRUE))
prob <- mkScalar(list.files(baseDir, pattern = ".probeset.csv",
full.names = TRUE))
trans <- mkScalar(list.files(baseDir, pattern = ".transcript.csv",
full.names = TRUE))
mpsFile <- mkScalar(list.files(baseDir, pattern = ".mps",
full.names = TRUE))
seed <- new("AffyGenePDInfoPkgSeed",
pgfFile = pgf, clfFile = clf,
probeFile = prob,
coreMps = mpsFile,
geneArray = TRUE,
transFile = trans,
version = "1.0.4",
chipName = "HuGene-1_0-st-v1",
manufacturer = "Affymetrix",
author="Peter White", email="peter.wh...@nationwidechildrens.org",
biocViews = "AnnotationData",
genomebuild="hg19",
organism = "Human", species = "Homo Sapiens",
url = "http://genomics.nchresearch.org/";)
makePdInfoPackage(seed, destDir=".")
Closed down R and went to the command prompt, navigated to the
appropriate directory:
R CMD INSTALL pd.hugene.1.0.st.v1
Next, I attempted to create the CDF file (I took one HuGene ST cel
file and put it in the working directory):
source("http://bioinf.wehi.edu.au/folders/mrobinson/aroma/PdInfo2Cdf.R";)
PdInfo2Cdf("pd.hugene.1.0.st.v1", "A1_Affy.CEL", overwrite=TRUE)
I renamed the resultin binary cdf file and moved it to the appropriate
aroma.affymetrix directory.
setwd("P:\\ANNOTATION\\aromaAffymetrix")
library(aroma.affymetrix)
chipType <- "HuGene-1_0-st-v1"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r4")
print(cdf)
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuGene-1_0-st-v1
Filename: HuGene-1_0-st-v1,r4.cdf
Filesize: 51.94MB
Chip type: HuGene-1_0-st-v1,r4
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 1050x1050
Number of cells: 1102500
Number of units: 253002
Cells per unit: 4.36
Number of QC units: 0
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grDevices datasets splines graphics stats tcltk utils
[8] methods base
other attached packages:
[1] aroma.affymetrix_1.5.0 aroma.apd_0.1.7 affxparser_1.18.0
[4] R.huge_0.2.0 aroma.core_1.5.0 aroma.light_1.15.1
[7] matrixStats_0.1.9 R.rsp_0.3.6 R.cache_0.2.0
[10] R.filesets_0.8.0 digest_0.4.2 R.utils_1.3.3
[13] R.oo_1.6.7 R.methodsS3_1.1.0 svSocket_0.9-48
[16] TinnR_1.0.3 R2HTML_1.59-1 Hmisc_3.7-0
[19] survival_2.35-8
loaded via a namespace (and not attached):
[1] cluster_1.12.1 grid_2.10.1 lattice_0.18-3 svMisc_0.9-56 tools_2.10.1
>
--
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