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Nathan.Watson | 1 Oct 2008 01:50
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Experimental Design Question(s)

I'm trying to understand and analyse a microarray experiment performed by someone else, and I've been
reading about experimental design in some books and have a few questions.

The experiment involves groups of animals assigned to one of 3 time points (measured as the number of days
since treatment) and administered with either A or B treatment. 2 out 3 tissue samples are taken from the
groups at their designated time point. This is basically to identify expression differences over a time
course in response to one of the two treatments. In addition a control group is used which received neither
A or B treatment and sampled at a single time point.

Am I correct in thinking I have an incomplete fractional factorial design since each group only has 2 of 3
possible tissue samples taken and it makes no sense to have control groups for ever time point and a control
can not be treated with either A or B? E.g. as mentioned at the bottom of this page:
http://www.socialresearchmethods.net/kb/expfact2.php

I was thinking of the below as a possible design. '-' no group possible as it's a control group

Tissue 1:
     days since treatment
      0    3    7    21
C     8    -    -    -
A     -    4    4    4
B     -    4    4    4

Tissue 2:
     days since treatment
      0    3    7    21
C     4    -    -    -
A     -    4    4    4
B     -    0    0    0
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Shi, Tao | 1 Oct 2008 02:43
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gene count in a GO term

Hi list,

Please forgive if this was asked before.

In R, is there a way to find out how many Human gene products in a GO term (including all its children) like
those reported in AmiGo?  I'm talking about ALL the gene products, not just those on a affy chip.  For
example, for GO:0005921 and children and its children, the number is 6.

Many thanks!

...Tao

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michael watson (IAH-C | 1 Oct 2008 10:16
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Re: gene count in a GO term

Well, you have to decide which database you believe!

For example, if you think Ensembl is correct, then use biomaRt 

-----Original Message-----
From: bioconductor-bounces@...
[mailto:bioconductor-bounces@...] On Behalf Of
Shi, Tao
Sent: 01 October 2008 01:43
To: bioconductor@...
Subject: [BioC] gene count in a GO term

Hi list,

Please forgive if this was asked before.

In R, is there a way to find out how many Human gene products in a GO
term (including all its children) like those reported in AmiGo?  I'm
talking about ALL the gene products, not just those on a affy chip.  For
example, for GO:0005921 and children and its children, the number is 6.

Many thanks!

...Tao

_______________________________________________
Bioconductor mailing list
Bioconductor@...
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
(Continue reading)

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m_kempenaar | 1 Oct 2008 10:16
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Need help using read.table to read in non-standard data

Hello,

I have a question about reading in data for use with the Limma package by using standard R functions like
read.table as mentioned in chapter 4.1.
The data I'm trying to use is an existing dataset from the DeRisi lab and will be used for educational
purposses only. I've been working on a script to preprocess/ normalize the data using standard R
functions after which I have a data frame containing the following columns (9 columns and 5969 rows):

ORF (Identifier)
Name (Gene name (optional))
T1 - T7 (normalized log intensities for each of the 7 arrays)

Other then the above I have no information about the data so I cannot create a targets.txt file etc. Is there
any way that I can use Limma to do the normalization and analysis on this data?

I'm trying to write a short tutorial on how to use Limma with this data which I hope to finish on friday, so any
help to point in the right direction is greatly appreciated.

M. Kempenaar
Bioinformatics
Hanze University
Groningen, the Netherlands

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michael watson (IAH-C | 1 Oct 2008 10:53
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Re: Need help using read.table to read in non-standard data

What are the actual data?  Raw intensities or log2 ratios?

You can either create an RGList object (if the data are raw intensities)
or an MAList object (if they are log ratios).  You could also create log
ratios from the data and then create an MAList object.

The problems comes if you only have data for one channel (red or
green?!) or you only have log ratios (where would you get A from?

We need more information

Mick 

-----Original Message-----
From: bioconductor-bounces@...
[mailto:bioconductor-bounces@...] On Behalf Of
m_kempenaar@...
Sent: 01 October 2008 09:17
To: bioconductor@...
Subject: [BioC] Need help using read.table to read in non-standard data

Hello,

I have a question about reading in data for use with the Limma package
by using standard R functions like read.table as mentioned in chapter
4.1.
The data I'm trying to use is an existing dataset from the DeRisi lab
and will be used for educational purposses only. I've been working on a
script to preprocess/ normalize the data using standard R functions
after which I have a data frame containing the following columns (9
(Continue reading)

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James W. MacDonald | 1 Oct 2008 14:14
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Re: gene count in a GO term

Hi Tao,

Shi, Tao wrote:
> Hi list,
> 
> Please forgive if this was asked before.
> 
> In R, is there a way to find out how many Human gene products in a GO
> term (including all its children) like those reported in AmiGo?  I'm
> talking about ALL the gene products, not just those on a affy chip.
> For example, for GO:0005921 and children and its children, the number
> is 6.

There are only 6 if you restrict to TAS and IDA. If you allow IEA then 
there are 27:

 > library(org.Hs.eg.db)
 > get("GO:0005921", org.Hs.egGO2ALLEGS)
         TAS         TAS         IEA         IEA         IEA         TAS
      "1823"      "2697"      "2700"      "2701"      "2702"      "2703"
         TAS         TAS         IEA         IEA         IEA         IEA
      "2705"      "2706"      "2707"      "2709"      "4284"      "9742"
         IEA         IEA         IEA         IEA         IEA         IEA
     "10052"     "10804"     "24145"     "56666"     "57165"     "57369"
         IEA         IEA         IEA         IDA         IEA         IEA
     "81025"     "84694"    "116337"    "125111"    "127534"    "219770"
         IEA         IEA         IEA
    "349149"    "375519" "100126572"

Best,
(Continue reading)

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James W. MacDonald | 1 Oct 2008 14:31
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Re: problem installing affycoretools in R in linux environment

Hi Manisha,

Manisha Brahmachary wrote:
> I also tried installing biomaRt separately but I was not able to do that. How
> do I get around this problem?
> 
> Please see the session below:
> 
> biocLite("biomaRt")
> Running biocinstall version 2.1.11 with R version 2.6.1 
> Your version of R requires version 2.1 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>   argument 'lib' is missing: using
> '/nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6'
> trying URL
> 'http://bioconductor.org/packages/2.1/bioc/src/contrib/biomaRt_1.12.2.tar.gz'
> Content type 'application/x-gzip' length 276683 bytes (270 Kb)
> opened URL
> ==================================================
> downloaded 270 Kb
> 
> /nfs/apollo/2/c2b2/users/mb3058/R/x86_64-unknown-linux-gnu-library/2.6
> * Installing *source* package 'biomaRt' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: RCurl
> Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
> lib.loc) :
(Continue reading)

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Claire d'iGraal | 1 Oct 2008 16:05

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J.Oosting | 1 Oct 2008 16:16
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Re: Need help using read.table to read in non-standard data

You should take a look at the limma analysis of affymetrix and other
single-channel designs, as this is what you have now basically.
The examples in the userguide on this type of data do not need a
targets.txt file.

Jan

> I have a question about reading in data for use with the Limma package
by
> using standard R functions like read.table as mentioned in chapter
4.1.
> The data I'm trying to use is an existing dataset from the DeRisi lab
and
> will be used for educational purposses only. I've been working on a
script
> to preprocess/ normalize the data using standard R functions after
which I
> have a data frame containing the following columns (9 columns and 5969
> rows):
> 
> ORF (Identifier)
> Name (Gene name (optional))
> T1 - T7 (normalized log intensities for each of the 7 arrays)
> 
> Other then the above I have no information about the data so I cannot
> create a targets.txt file etc. Is there any way that I can use Limma
to do
> the normalization and analysis on this data?
> 
> I'm trying to write a short tutorial on how to use Limma with this
(Continue reading)

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Shi, Tao | 1 Oct 2008 19:50
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Re: gene count in a GO term

Thanks, Jim and Michael, for the speedy replies!

Following up Michael's point, I tried biomaRt, but the number of genes seems way too low comparing what
reported on geneontology webpage (see below).  I'm not sure how they're mapped.  "org.Hs.eg.db" gave
comparable number, which is not surprising as it derived directly from the gene ontology site.

###=====================================================================
## GO:0005575 is the root term for CC, there are 9428 gene product according to AmiGo
##======================================================================
>   mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
Checking attributes and filters ... ok
>    tmp <- getBM(attributes=c( "ensembl_gene_id"), filters="go",values="GO:0005575", mart = mart)
>    dim(tmp)
[1] 641   1
>     tmp <- getBM(attributes=c( "entrezgene"), filters="go",values="GO:0005575", mart = mart)
>     dim(tmp)
[1] 565   1

...Tao

----- Original Message ----
From: James W. MacDonald <jmacdon@...>
To: "Shi, Tao" <shidaxia@...>
Cc: bioconductor@...
Sent: Wednesday, October 1, 2008 5:14:13 AM
Subject: Re: [BioC] gene count in a GO term

Hi Tao,

Shi, Tao wrote:
(Continue reading)

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