Dear Mark,
I am using the HuGene-1_0-st-v1.r4 clf and pgf files. When I run the
script it just returns a stream of repeated errors, until terminated:
>\\ANNOTATION\AffyAnnotation\Human\HuGene-1_0-st-v1>perl combineProbeInfo.pl
>HuGene-1_0-st-v1.r4
Use of uninitialized value in exists at combine
For Gene ST arrays it appears that pdInfoBuilder will not work if a
transFile argument is specified. Secondly, in the example above
probeFile = "HuGene-1_0-st-v1.probe.tab" is incorrect - it should be
the *.probeset.csv file from Affy. And finally, it also requires that
the MPS (Meta Probeset File)
does the Fusion SDK library, which affxparser is using, fail
> >> to extract the filename, i.e. fail to drop the path from the full
> >> pathname. It is likely that the backslashes at the beginning cause
> >> this problem.
> >>
> >> As a workaround for now, beca
n LIbrary
setwd("P:\\ANNOTATION\\AffyAnnotation\\Human\\HG-U133_Plus_2")
library(pdInfoBuilder)
cdfFile <- "HG-U133_Plus_2.cdf"
csvAnnoFile <- "HG-U133_Plus_2.na27.annot.csv"
tabSeqFile <- "HG-U133_Plus_2.probe_tab"
pkg <- new("AffyExpression
probesets. I'm
> happy to go and collect these if people want them, but based on the
> reply from Affymetrix (thanks to Mark Cowley for the leg work here),
> they are probably 'low-coverage transcript clusters' that can be
> 'safely ignored'. See:
>
27 27 27
> >> 8095005 42 42 42
> >> 8100310 10 10 10
> >> 7948117 15 15 15
> >> 8155877 25 25 25
> >>> table(matches[,3]-matches
ays: 10
Names: AFX_1_A1, AFX_1_A2, ..., AFX_1_B5
Time period: 2005-09-07 12:01:05 -- 2005-09-07 14:03:23
Total file size: 129.23MB
RAM: 0.01MB
On Dec 4, 11:19 am, pwhiteusa <[EMAIL PROTECTED]> wrote:
> Sorry, just one more follow up on the shortcuts. Is it correct that
> they will on
use shortcuts to the actual cel files and that didn't work out either.
On Dec 4, 8:48 am, pwhiteusa <[EMAIL PROTECTED]> wrote:
> Hi Henrik,
>
> It worked!!! Thanks so much for working through it with me - I really
> appreciate it. I was a little frustrated with the aroma.affyme
1
On Dec 3, 11:04 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> On Wed, Dec 3, 2008 at 6:36 AM, pwhiteusa <[EMAIL PROTECTED]> wrote:
>
> > Sorry I missed the 0 and -1 at the edge of the screen. See below, but
> > basically when the mode
ost there. Unfortunately, you left out the one answer I
> was most interest in; see below.
>
>
>
> On Tue, Dec 2, 2008 at 12:34 PM, pwhiteusa <[EMAIL PROTECTED]> wrote:
>
> > Hi Henrik,
>
> > The results are interspersed below:
>
> > On Nov 26, 4:27
. No annotation chip type file with that chip type found:
MoGene-1_0-st-v1
at throw(Exception(...))
at throw.default("Could not create ", class(static)[1], " object. No
annotatio
at throw("Could not create ", class(static)[1], " object. No
annotation chip t
at m
Hi All,
Here is the exact code I used to analyze Gene ST data for an
experiment performed with the MoGene-1_0-st-v1 array.
AROMA.AFFYMETRIX
library(aroma.affymetrix)
cdf <- AffymetrixCdfFile$fromChipType("MoGene-1_0-st-v1",tags="r3")
prefixName <- "Pierson"
cs <- AffymetrixCelSet$byName(prefixN
Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
>
> > Hi,
>
> > one typo by me, please retry with:
>
> > path2 <- filePath(path, "chipTypes", "MoGene-1_0-st-v1");
>
> > [I forgot 'chipTypes']
>
> > /Henrik
Peter
On Nov 24, 2:59 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> one typo by me, please retry with:
>
> path2 <- filePath(path, "chipTypes", "MoGene-1_0-st-v1");
>
> [I forgot 'chipTypes']
>
> /Henrik
>
The answers are dispersed below
> > I just wanted to update you on the issue of creating Windows shortcuts
> > to point to the correct directory.
>
> > So the CDF files I want to use is on a mapped network drive - it is
> > mapped to my "P Drive":
>
> > P:\ANNOTATION\aromaAffymetrix\annot
annotationData")
[1] "C:/annotationData"
If there is a way around it that's great, but if not I can live with
just creating a copy of the annotation data on on my local machine.
Thought I should post my experience in case others go through the
same.
Thanks,
Peter
On Oct 22, 4
Dear Henrik and Mark,
Thanks so much for your replies. I am going to work through your
responses and try again. I did get confused by the directory structure
and naming conventions. What I would like to do is have all of my
annotation files in one location (Network Drive W) as these are shared
by
Is there a vignette for analyzing data from the Gene ST arrays? I am
processing some HuGene10st arrays. This is what I came up with so far, but
am stuck with regard to how to write the normalized data set as a table or
to create an R object:
#Convert CDF downloaded from Affy from ASCII to Binary f
To get the plotImage commands to work I had to first install
ImageMagick (http://www.imagemagick.org/script/binary-
releases.php#windows), then GTK+ (http://sourceforge.net/projects/gtk-
win/) and finally GPL Ghostscript (http://pages.cs.wisc.edu/~ghost/doc/
GPL/index.htm). Restart windows and sta
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