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Why is the affy version in the developmental packages 1.1 now? A
couple
of months ago it was 1.2
0
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Laurent Gautier
★
2.3k
@laurent-gautier-29
Last seen 10.3 years ago
On Wed, Nov 20, 2002 at 11:39:00AM -0500, Isaac Neuhaus wrote:
> Why is the affy version in the developmental packages 1.1 now? A
couple
> of months ago it was 1.2
>
Dear Isaac,
The version numbering was subject to a floating policy up to a very
recent
time (and the decision that the new release for BioC would be 1.1).
The version number has probably been changed to match that (I
assume...)
The version 1.1 of affy is both the released and developmental version
for
the moment.
Laurent
0
Entering edit mode
Hi all!
Can someone explain to my why the hist function applied to the
expression values returns less values, i.e. less genes, than there are
on the hu68 chip?
Here my code fragments:
> Mydata <- ReadAffy(CDFfile="hu6800.cdf",...)
> Mydata.rma <- express(Mydata)
> dim(exprs(Mydata.rma))
[1] 7129 18
# ok, here we have 7129 expression values
> Mydata.rma.hist <- hist(exprs(Mydata.rma),,plot=F)
> sum(Mydata.rma.hist$counts)
[1] 42774
# here we are down to 42774 genes
Cheers,
Hinnerk
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22.1 years ago
Hinnerk Boriss
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220
0
Entering edit mode
Hi Hinnerk,
what's
length(whichis.na(exprs(Mydata.rma))))
respectively
length(which(!is.na(exprs(Mydata.rma))))
???
Best regards
Wolfgang Huber
w.huber@dkfz.de
http://www.dkfz.de/abt0840/whuber
Tel +49-6221-424709
Fax +49-6221-42524709
DKFZ, Division of Molecular Genome Analysis
69120 Heidelberg, Germany
-----Original Message-----
From: bioconductor-admin@stat.math.ethz.ch
[mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Hinnerk
Boriss
Sent: Thursday, November 21, 2002 11:21 AM
To: 'Bioconductor'
Subject: [BioC] data reduction in "hist" function?
Hi all!
Can someone explain to my why the hist function applied to the
expression values returns less values, i.e. less genes, than there are
on the hu68 chip?
Here my code fragments:
> Mydata <- ReadAffy(CDFfile="hu6800.cdf",...)
> Mydata.rma <- express(Mydata)
> dim(exprs(Mydata.rma))
[1] 7129 18
# ok, here we have 7129 expression values
> Mydata.rma.hist <- hist(exprs(Mydata.rma),,plot=F)
> sum(Mydata.rma.hist$counts)
[1] 42774
# here we are down to 42774 genes
Cheers,
Hinnerk
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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22.1 years ago
Wolfgang Huber
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0
Entering edit mode
Hi Wolfgang!
> length(whichis.na(exprs(Mydata.rma))))
returns: 0
> length(which(!is.na(exprs(Mydata.rma))))
returns: 128322 which is just three times sum(Mydata.rma.hist$counts)
=
42774.
Why???? Does that help?
Best,
Hinnerk
>
>
> Hi all!
>
> Can someone explain to my why the hist function applied to the
> expression values returns less values, i.e. less genes, than there
are
> on the hu68 chip?
>
> Here my code fragments:
>
> > Mydata <- ReadAffy(CDFfile="hu6800.cdf",...)
> > Mydata.rma <- express(Mydata)
> > dim(exprs(Mydata.rma))
> [1] 7129 18
> # ok, here we have 7129 expression values
>
> > Mydata.rma.hist <- hist(exprs(Mydata.rma),,plot=F)
> > sum(Mydata.rma.hist$counts)
> [1] 42774
> # here we are down to 42774 genes
>
> Cheers,
> Hinnerk
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
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22.1 years ago
Hinnerk Boriss
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