Displaying 4 results from an estimated 4 matches for "ath1121501".
2007 Apr 28
1
normalizing affy data caused an error
...ut 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!
4: missing cdf environment! in show(AffyBatch)
> sessio...
2011 Aug 08
1
read in cel file by ReadAffy and read.celfile
...=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "X" "Y"
$ MULTICHANNEL: logi TRUE
$ CHANNELNAMES: chr [1:2] "531" "609"
My question is
1. why ReadAffy doesn't work for this chip? is that because of the cel file
type?
2. I have some experience of ATH1121501 chip analysis, the data
structure given by read.celfile looks different from that, how to get PM/MM
values?
Any help will be highly appreciated!
Na
[[alternative HTML version deleted]]
2008 Dec 10
0
FW: Kegg.db with GOstats
...wrote:
> Dear Robert Gentleman,
> I am currently working on Streptomyces coelicolor microarray data.
>
> I have some clusters of genes and I would like to annotate them, but as you may know, this organism is not yet annotated with Gene Ontologies. There is no database (such as at "ath1121501.db" for Arabidopsis thaliana) available to use with the GOstats package.
>
> So, I would like to use at least the Kegg.db package with GOstats.
> Can you tell me how to include KEGG.db ? I can't find anything about it.
>
> Thank you very much.
> Roxane LEGAIE.
>
>...
2012 Nov 07
0
Annotation using org.At.tair.db package in R
...36
I would like to extract only the first column as follows :
ids <- scr[,2]
and then I got a factor[2368]
And then I proceeded to the annotation as follows:
biocLite("GO.db")
library("AnnotationDbi")
biocLite("org.At.tair.db")
biocLite("ath1121501.db").
genenames <- org.At.tairGENENAME[ids] #map the probe ids to the gene
names in TAIR
The output of which is AnnDbBiMap[1]
number<-org.At.tairENTREZID[ids] #map the probe ids to the gene ids in
TAIR
The output of which is AnnDbBiMap[1]
And then I try to m...