Entering edit mode
Keith James
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10
@keith-james-2235
Last seen 10.2 years ago
I am reading single channel bead level data using the readIllumina
function.
The docs indicate that there is a path parameter:
path character string specifying the location of files to be read
by the
function
Calling the function with a path argument results in an error:
readIllumina(path = "/path/to/data", txtType = ".txt")
Error in strtrim(x, width) : invalid 'width' argument
> traceback()
4: strtrim(xyFiles, nchar(xyFiles) - 4)
3: as.vector(y)
2: intersect(strtrim(GImages, nchar(GImages) - 8), strtrim(xyFiles,
nchar(xyFiles) - 4))
1: readIllumina(path = "/path/to/data", txtType = ".txt")
I've seen in another post that readIllumina expects the files to be in
the
working directory, and this is the case since this line in the
function
relies on the default path for dir calls:
GImages = dir(pattern = "_Grn.tif")
At first I took this to be a documentation bug, but in fact the path
argument
is honoured for loading the csv files:
file = csv_files[i]
if (!is.null(path))
file = file.path(path, file)
and the annotation (.opa file):
if (!is.null(path))
annoFile = file.path(path, annoFile)
but apparently not for loading the metrics file:
if (metrics) {
metrics = dir(pattern = metricsFile)
My suggestion is to make the behaviour consistent across all the data,
i.e. to
honour a path argument for tif and metrics files.
It is probably worth noting in the docs the assumptions the function
makes
about the files it expects in the data directory. i.e. that *all* tif
images
will be loaded and *all* .txt files. My data directory contained other
.tif
and .txt files ("targets.txt", "notes.txt") which caused the function
to
choke. I think that it is optimistic to assume that users will have no
other
such files present.
In addition, I wonder whether the column names in the csv/txt files
vary with
the version of the scanner or scanner software. Instead of
ProbeID G Gb GrnX GrnY
or similar, we have
Code Grn GrnX GrnY
So, 4 columns rather than 3 or 5.
Finally, we appreciate all the work you've done in enabling us to work
with
raw Illumina data. Many thanks.
> sessionInfo()
R version 2.5.0 (2007-04-23)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_GB;LC_NUMERIC=C;LC_TIME=en_GB;LC_COLLATE=en_GB;LC_MONETARY
=en_GB;LC_MESSAGES=en_GB;LC_PAPER=en_GB;LC_NAME=C;LC_ADDRESS=C;LC_TELE
PHONE=C;LC_MEASUREMENT=en_GB;LC_IDENTIFICATION=C
attached base packages:
[1] "grid" "tools" "stats" "graphics" "grDevices"
"utils"
[7] "datasets" "methods" "base"
other attached packages:
beadarray beadarraySNP quantsmooth lodplot quantreg
SparseM
"1.4.0" "1.2.0" "1.2.0" "1.1" "4.06"
"0.73"
affy affyio geneplotter lattice annotate
Biobase
"1.14.0" "1.4.0" "1.14.0" "0.15-4" "1.14.1"
"1.14.0"
limma
"2.10.0"
--
- Keith James <kdj at="" sanger.ac.uk=""> Microarray Informatics Group -
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK -
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
