Displaying 3 results from an estimated 3 matches for "affyids".
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affairs
2011 Feb 25
1
limma function problem
Hi,
I have two data set of normalized Affymetrix CEL files, wild type vs Control
type.(each set have further three replicates).
> wild.fish
AffyBatch object
size of arrays=712x712 features (10 kb)
cdf=Zebrafish (15617 affyids)
number of samples=3
number of genes=15617
annotation=zebrafish
notes=
> Dicer.fish
AffyBatch object
size of arrays=712x712 features (10 kb)
cdf=Zebrafish (15617 affyids)
number of samples=3
number of genes=15617
annotation=zebrafish
notes=
Now, I have to combine these two S4 objects and use lm...
2007 Apr 28
1
normalizing affy data caused an error
...a
Linux server. When I read in the cel files all seemed ok. But the next
step caused an error. With Win XP all works fine. Did anyone experience
similar problems?
Thanks,
Thomas
> PI <- ReadAffy()
> PI
AffyBatch object
size of arrays=712x712 features (14 kb)
cdf=ATH1-121501 (??? affyids)
number of samples=6
number of genes=506944
annotation=ath1121501
notes=
Warning messages:
1: Line starting '<TITLE>Error</TITLE> ...' is malformed!
2: Line starting '<BODY> ...' is malformed!
3: Line starting '<H1>Error</H1> ...' is malformed!...
2006 Jul 25
1
Drosophila Genome 2.0 annaffy annotation
...est affy Drosophila
2.0 GeneChip. I am trying to run simple annaffy analysis but can¹t find what
is the name of the annotation file I need to use.
Here is the output of the AffyBatch object I am using:
> expData
AffyBatch object
size of arrays=732x732 features (16749 kb)
cdf=Drosophila_2 (18952 affyids)
number of samples=4
number of genes=18952
annotation=drosophila2
So when I try to use and annaffy procedure I get:
>Symbol = aafSymbol(geneIDs, "drosophila2")
[1] "You are missing drosophila2 looking to see if it is available."
Error in chkPkgs(chip) : couldn''t fi...