Dear all,
please could you let me know whether there is any major updates in the
newest version of edgeR
(for Bioconductor version: Release (2.13),
http://www.bioconductor.org/packages/2.13/bioc/html/edgeR.html), as I
am
getting a lot less Differentially Expressed Genes than before ...
thanks !
-- bogdan
[[alternative HTML version deleted]]
Hi,
On Mon, Dec 2, 2013 at 2:20 PM, Bogdan Tanasa <tanasa at="" gmail.com="">
wrote:
> Dear all,
>
> please could you let me know whether there is any major updates in
the
> newest version of edgeR
> (for Bioconductor version: Release (2.13),
> http://www.bioconductor.org/packages/2.13/bioc/html/edgeR.html), as
I am
> getting a lot less Differentially Expressed Genes than before ...
When was "before" (ie. what previous version are you trying to compare
to?)
Also, this will help:
R> news(package="edgeR")
-steve
--
Steve Lianoglou
Computational Biologist
Genentech
Thanks, Steve ...I was referring to the edgeR version of April 2012.
On Mon, Dec 2, 2013 at 2:27 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:
> Hi,
>
> On Mon, Dec 2, 2013 at 2:20 PM, Bogdan Tanasa <tanasa@gmail.com>
wrote:
> > Dear all,
> >
> > please could you let me know whether there is any major updates in
the
> > newest version of edgeR
> > (for Bioconductor version: Release (2.13),
> > http://www.bioconductor.org/packages/2.13/bioc/html/edgeR.html),
as I am
> > getting a lot less Differentially Expressed Genes than before ...
>
> When was "before" (ie. what previous version are you trying to
compare to?)
>
> Also, this will help:
>
> R> news(package="edgeR")
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>
[[alternative HTML version deleted]]
edgeR is updated all the time. There have been no changes that make
the
package much less sensitive, but the default value for the dispersion
prior weight was changed some time ago as was the syntax for
specifying
the prior weight. See help for prior.df in estimateTagwispDisp() and
estimateGLMTagwiseDisp(). The prior.df determines the amount of
squeezing
that is applied to the tagwise dispersion values.
Hi there,
I am making my way through the edgeR User's Guide. In chapter 4.4 I
use the Tuch data set as follows:
rawdata<-read.delim("H:/bip1/RNAseq/Data/TableS1.txt",check.name=FALSE
,stringsAsFactors=FALSE)
head(rawdata)
dim(rawdata)
# read the data
y<-DGEList(counts=rawdata[,4:9],genes=rawdata[,1:3])
str(y)
# Annotation
library(org.Hs.eg.db)
idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)
y<-y[idfound,]
dim(y)
According to the User's Guide the dimension of the y-matrix after
removing those not having a NCBI annotation, should be 15577 x 6.
However, when I use the User's Guide code, I end up with a y-matrix
with dimension 0 x 6.
I'm afraid I need help to figure out what I am doing wrong here.
Thank you.
jahn
-- output of sessionInfo():
> rawdata<-read.delim("H:/bip1/RNAseq/Data/TableS1.txt",check.name=FAL
SE,stringsAsFactors=FALSE)
>
> head(rawdata)
RefSeq Symbol NbrOfExons 8N 8T 33N 33T 51N 51T
1 NM_182502 TMPRSS11B 10 2592 3 7805 321 3372 9
2 NM_003280 TNNC1 6 1684 0 1787 7 4894 559
3 NM_152381 XIRP2 10 9915 15 10396 48 23309 7181
4 NM_022438 MAL 3 2496 2 3585 239 1596 7
5 NM_001100112 MYH2 40 4389 7 7944 16 9262 1818
6 NM_017534 MYH2 40 4402 7 7943 16 9244 1815
> dim(rawdata)
[1] 15668 9
> y<-DGEList(counts=rawdata[,4:9],genes=rawdata[,1:3])
> idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)
> y<-y[idfound,]
> dim(y)
[1] 0 6
>
--
Sent via the guest posting facility at bioconductor.org.
Hi Jahn,
Note that the name of the first column of your data is RefSeq, and you
are subsetting on RefSeqID, which doesn't appear to exist.
Best,
Jim
On Tuesday, December 17, 2013 1:34:28 AM, Jahn Davik [guest] wrote:
>
> Hi there,
> I am making my way through the edgeR User's Guide. In chapter 4.4 I
use the Tuch data set as follows:
>
> rawdata<-read.delim("H:/bip1/RNAseq/Data/TableS1.txt",check.name=FAL
SE,stringsAsFactors=FALSE)
>
> head(rawdata)
> dim(rawdata)
>
> # read the data
> y<-DGEList(counts=rawdata[,4:9],genes=rawdata[,1:3])
>
> str(y)
> # Annotation
>
> library(org.Hs.eg.db)
>
> idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)
>
> y<-y[idfound,]
>
> dim(y)
>
>
> According to the User's Guide the dimension of the y-matrix after
removing those not having a NCBI annotation, should be 15577 x 6.
However, when I use the User's Guide code, I end up with a y-matrix
with dimension 0 x 6.
> I'm afraid I need help to figure out what I am doing wrong here.
>
> Thank you.
> jahn
>
>
>
>
> -- output of sessionInfo():
>
>> rawdata<-read.delim("H:/bip1/RNAseq/Data/TableS1.txt",check.name=FA
LSE,stringsAsFactors=FALSE)
>>
>> head(rawdata)
> RefSeq Symbol NbrOfExons 8N 8T 33N 33T 51N 51T
> 1 NM_182502 TMPRSS11B 10 2592 3 7805 321 3372 9
> 2 NM_003280 TNNC1 6 1684 0 1787 7 4894 559
> 3 NM_152381 XIRP2 10 9915 15 10396 48 23309 7181
> 4 NM_022438 MAL 3 2496 2 3585 239 1596 7
> 5 NM_001100112 MYH2 40 4389 7 7944 16 9262 1818
> 6 NM_017534 MYH2 40 4402 7 7943 16 9244 1815
>> dim(rawdata)
> [1] 15668 9
>> y<-DGEList(counts=rawdata[,4:9],genes=rawdata[,1:3])
>> idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)
>> y<-y[idfound,]
>> dim(y)
> [1] 0 6
>>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
