Sorry another question,
What is the sign.matrix in your table construction?
On Sep 11, 4:43 pm, zrl wrote:
> Hi Math,
>
> Thank you for your detailed information, I begin to know how to
> process them.
> After I run:
>
> cesTr <- getChipEffectSet(plmTr)
>
> trFit <- extractDataFrame(cesTr, units
Hi Math,
Thank you for your detailed information, I begin to know how to
process them.
After I run:
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
the trFit has several columns
head(trFit)
unitName groupName unit group cell Grp6 Grp7 Grp8
1 231
On Fri, Sep 11, 2009 at 8:26 AM, mbaudis wrote:
>
> Dear all,
>
> how can I access a vector containing all array names used during
> processing?
getNames(cbs)
>
> Also, can one run the segmentation not by chromosome, but by array (or
> specify both)?
Did you try:
reg <- getRegions(cbs, arrays
Opps, missed one line in that demo code:
library("R.cache");
pathname <- saveCache(key=list("foo"), 1:9);
cat(file=pathname, "Make file corrupt");
res <- loadCache(key=key); cat("Still running...\n");
print(res); # NULL
/H
On Fri, Sep 11, 2009 at 11:49 AM, Henrik Bengtsson
wrote:
> On Mon, Se
On Mon, Sep 7, 2009 at 4:37 AM, mbaudis wrote:
>
> Henrik,
>
> thanks for the comments.
>
>> Just so we are one the same page, deleting .Rcache/ directory does not
>> make R consume more memory, but rather less.
>
> To clarify, deleting of the cached files was not done due to the
> memory issues
Hi !
I managed to do this by using the public annotations on the affymetrix
website (netaffx i believe). Its far away in my memory, but they provide a
format that is like..
1 // 2 // 3 // 4 /// 1 // 2 // 3 // 4
This is probably not the best way but it worked for me... Just adapt it to
your needs
Hi,
Try using getNames, e.g.
getNames(cesN)
Cheers,
Pierre.
On Fri, Sep 11, 2009 at 8:26 AM, mbaudis wrote:
>
> Dear all,
>
> how can I access a vector containing all array names used during
> processing?
>
> Also, can one run the segmentation not by chromosome, but by array (or
> specify
Hi Math,
Thank you for your reply. But I still can not figure out how to
annotate the results, i.e. from summarization results to genes/
transcripts info. Could you help me out? I am used to using
bioconductor, but aroma doesn't use the same classes (such as
affybatch or expressionSet).
Thank you
Dear all,
how can I access a vector containing all array names used during
processing?
Also, can one run the segmentation not by chromosome, but by array (or
specify both)? I could extract the names from the regions file after
segmentation
levels(names(reg))
but would miss out on arrays witho
Hey !
Here is the link to the aroma.affymetrix step by step analysis of human exon
arrays.
http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis
cheers,
Math
On Thu, Sep 10, 2009 at 6:19 PM, zrl wrote:
>
> Dear Group,
>
> I am current starting to analyze some human affy
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