headers
Peter Robinson | 1 Mar 2009 11:14
Picon
Favicon

Cannot find MoGene-1.0

Hi all,

I am trying to use the affy package to analyze  GeneChip® Mouse Gene 1.0 
ST Array data.  What do I need to do to get the CDF information for this 
chip? I am loading the
mogene10st.db package, but that doesnt seem to be correct.
Thanks a lot, Peter

 > library(affy)
Lade nötiges Paket: Biobase
Lade nötiges Paket: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Lade nötiges Paket: affyio
Lade nötiges Paket: preprocessCore

 > library(mogene10st.db)
Lade nötiges Paket: AnnotationDbi
Lade nötiges Paket: DBI
 > myAffy = ReadAffy(filenames=celfiles)

 > myAffy
AffyBatch object
size of arrays=1050x1050 features (11 kb)
cdf=MoGene-1_0-st-v1 (??? affyids)
(Continue reading)

Permalink | Reply | 1 comment |
headers
Sean Davis | 1 Mar 2009 13:41
Picon

Re: Cannot find MoGene-1.0

On Sun, Mar 1, 2009 at 5:14 AM, Peter Robinson
<peter.robinson@...>wrote:

> Hi all,
>
> I am trying to use the affy package to analyze  GeneChip® Mouse Gene 1.0 ST
> Array data.  What do I need to do to get the CDF information for this chip?
> I am loading the
> mogene10st.db package, but that doesnt seem to be correct.
> Thanks a lot, Peter
>
> > library(affy)
> Lade nötiges Paket: Biobase
> Lade nötiges Paket: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Lade nötiges Paket: affyio
> Lade nötiges Paket: preprocessCore
>
> > library(mogene10st.db)
> Lade nötiges Paket: AnnotationDbi
> Lade nötiges Paket: DBI
> > myAffy = ReadAffy(filenames=celfiles)
>
> > myAffy
(Continue reading)

Permalink | Reply | 0 comments |
headers
Jacek Nowak | 1 Mar 2009 21:01
Picon

justGCRMA problem :(

Hi!
I'm still getting an error after running justGCRMA:

Computing affinities.Done.
Adjusting for optical effect.........................Done.
Adjusting for non-specific binding........................Done.
Error in just.gcrma(filenames = l$filenames, phenoData = l$phenoData,  :
  INTEGER() can only be applied to a 'integer', not a 'language'

> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=pl_PL.UTF-8;LC_NUMERIC=C;LC_TIME=pl_PL.UTF-8;LC_COLLATE=pl_PL.UTF-8;LC_
              MONETARY=C;LC_MESSAGES=pl_PL.UTF-8;LC_PAPER=pl_PL.UTF-8;LC_NAME=C;LC_ADDRESS=C;L
              C_TELEPHONE=C;LC_MEASUREMENT=pl_PL.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] hgu133plus2probe_2.0.0 hgu133plus2cdf_2.3.0   gcrma_2.15.3
[4] matchprobes_1.10.0     affy_1.16.0            preprocessCore_1.0.0
[7] affyio_1.11.3          Biobase_1.16.3

loaded via a namespace (and not attached):
[1] splines_2.8.1
(Continue reading)

Permalink | Reply | 501 comments |
headers
Martin Morgan | 1 Mar 2009 21:28

Re: justGCRMA problem :(

Hi Jacek --

Jacek Nowak <losowy@...> writes:

> Hi!
> I'm still getting an error after running justGCRMA:
>
> Computing affinities.Done.
> Adjusting for optical effect.........................Done.
> Adjusting for non-specific binding........................Done.
> Error in just.gcrma(filenames = l$filenames, phenoData = l$phenoData,  :
>   INTEGER() can only be applied to a 'integer', not a 'language'
>
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=pl_PL.UTF-8;LC_NUMERIC=C;LC_TIME=pl_PL.UTF-8;LC_COLLATE=pl_PL.UTF-8;LC_
>               MONETARY=C;LC_MESSAGES=pl_PL.UTF-8;LC_PAPER=pl_PL.UTF-8;LC_NAME=C;LC_ADDRESS=C;L
>               C_TELEPHONE=C;LC_MEASUREMENT=pl_PL.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] hgu133plus2probe_2.0.0 hgu133plus2cdf_2.3.0   gcrma_2.15.3
> [4] matchprobes_1.10.0     affy_1.16.0            preprocessCore_1.0.0
> [7] affyio_1.11.3          Biobase_1.16.3
(Continue reading)

Permalink | Reply | 501 comments |
headers
Manhong Dai | 2 Mar 2009 15:28
Picon

Re: Cannot find MoGene-1.0

Hi Peter,

	This chip is supported in Custom CDF version 11, you can google 'custom
cdf' for detail.

Best,
Manhong
> Date: Sun, 01 Mar 2009 11:14:50 +0100
> From: Peter Robinson <peter.robinson@...>
> Subject: [BioC] Cannot find MoGene-1.0
> To: Bioconductor@...
> Message-ID: <49AA601A.90204@...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hi all,
> 
> I am trying to use the affy package to analyze  GeneChip? Mouse Gene 1.0 
> ST Array data.  What do I need to do to get the CDF information for this 
> chip? I am loading the
> mogene10st.db package, but that doesnt seem to be correct.
> Thanks a lot, Peter
> 
>  > library(affy)
> Lade n?tiges Paket: Biobase
> Lade n?tiges Paket: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
(Continue reading)

Permalink | Reply | 0 comments |
headers
Amy Johnson | 2 Mar 2009 15:34
Picon

Heatmap hints and identifying differentially expressed genes

Hi,

I'm new to biostatistics and R programming. I need some help for heatmap or 
heatmap.2 functions, especially I'm confused about the color settings. 
Here is what I'm trying to do: I have microarray data with several groups 
of treated samples and one group of control samples. I have calculated 
the averaged intensity of each gene in each group and calculated the 
simple fold change by comparing it to corresponding gene in the control 
group. I have picked the activated genes (>2-fold) and repressed genes 
(<0.5-fold). Now I need to show my boss of the fold changes in heatmap. 
I'd like to shown genes with fold changes < 1 in blue gradient color and 
genes with fold changes > 1 in red gradient color. Genes with 
fold-changes close to 1 in yellow color. How do I specify the color 
parameter in heatmap (or heatmap.2) function? 

Heat is my code (not working):

data <- read.csv("mydata.csv", header=TRUE);
library(gplots);
x <- as.matrix(data);
heatmap.2(x, Rowv=FALSE, Colv=FALSE, col=rev(redgreen(100)), key=FALSE, 
trace="none", dendrogram="none");

mydata.csv is like this:

treat1,treat2,treat3
GREB1,9.3,6.47,5.37
SUSD3,7.95,3.41,3.64
FOS,6.68,15.91,18.02
GAL,3.63,1.19,1.33
(Continue reading)

Permalink | Reply | 2 comments |
headers
Marietta Herrmann | 2 Mar 2009 16:10
Picon
Picon

Re: Heatmap hints and identifying differentially expressed genes

Hi Amy,

you can set up every color you want with this command:

mycolors<-function(n) colorpanel(n, "blue", "white", "brown")

you can fit in every color from the R color chart, which you can find here:
http://research.stowers-institute.org/efg/R/Color/Chart/

in the heatmap-command you set col=mycolors(32)

I hope this helps you!

Best regards,

Marietta Herrmann

Am 3/2/09 3:34 PM schrieb "Amy Johnson" unter <a7johnson@...>:

> Hi,
> 
> I'm new to biostatistics and R programming. I need some help for heatmap or
> heatmap.2 functions, especially I'm confused about the color settings.
> Here is what I'm trying to do: I have microarray data with several groups
> of treated samples and one group of control samples. I have calculated
> the averaged intensity of each gene in each group and calculated the
> simple fold change by comparing it to corresponding gene in the control
> group. I have picked the activated genes (>2-fold) and repressed genes
> (<0.5-fold). Now I need to show my boss of the fold changes in heatmap.
> I'd like to shown genes with fold changes < 1 in blue gradient color and
(Continue reading)

Permalink | Reply | 0 comments |
headers
Steve Lianoglou | 2 Mar 2009 16:30
Picon

Re: Heatmap hints and identifying differentially expressed genes

Hi,

> Here is another quick question: how do I calculate the p-value for  
> each
> gene? I'm simply calculating the fold-changes. But it is better to do
> some kinds of statistical analysis. In my experiment, each sample  
> group
> is in triplicate. What is the best way to pick up differentially
> expressed genes (not using fold changes)?

Yeah, just fixing a global threshold of fold change for differential  
expression isn't really the best. For a relatively easy way to get  
differentially expressed genes, look into the limma package:

http://www.bioconductor.org/packages/2.3/bioc/html/limma.html

It'll get you the p-values you're after, as well.

Hope that helps,

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos

_______________________________________________
(Continue reading)

Permalink | Reply | 0 comments |
headers
Sean Davis | 2 Mar 2009 17:30
Picon

Re: Heatmap hints and identifying differentially expressed genes

On Mon, Mar 2, 2009 at 10:24 AM, Amy Johnson <a7johnson@...> wrote:

> Hi,
>
> Thanks for your quick response. How do I specify colors corresponding to
> values, e.g. 0-1 (blue to yellow gradient), 1 (yellow), 1-10(yellow to
> red gradient)?
>

You'll want to play with the breaks argument.  There are a number of posts
in the archives that may be useful.

Sean

>
>
> ----- Original Message -----
> From: "Marietta Herrmann" <mariherrmann@...>
> To: Amy Johnson <a7johnson@...>, bioconductor@...
> Date: Mon, Mar 2, 2009 at 10:10 AM
> Subject: Heatmap hints and identifying differentially expressed genes
>
> > Hi Amy,
> >
> > you can set up every color you want with this command:
> >
> > mycolors<-function(n) colorpanel(n, "blue", "white", "brown")
> >
> > you can fit in every color from the R color chart, which you can find
> here:
(Continue reading)

Permalink | Reply | 0 comments |
headers
Kasper Daniel Hansen | 2 Mar 2009 17:47
Picon

Re: Graphviz in Vista64

Most likely something is wrong with your graphviz installation, but  
since you don't provide any details about that, it is impossible to  
help. We would also like to see the actual crash output from R or a  
better description of what you mean by "crash"

Kasper

On Mar 2, 2009, at 7:48 , Sim, Fraser wrote:

> Hi Bioconductors,
>
> Has anyone successfully used the Rgraphviz package to plot graphs in R
> under Vista64??
>
> I have found that RGUI.EXE crashes upon execution of the layoutGraph
> step.
>
> Running the following reliably crashes R.
>
> library("Rgraphviz")
> g = new("graphNEL", nodes = c("a","b","c"))
> debug(Rgraphviz:::graphLayout)
> sessionInfo()
> layoutGraph(g)
>
> Thanks,
> Fraser
>
> PS. The crash occurs in :
>
(Continue reading)

Permalink | Reply | 0 comments |

Gmane