[BioC] Comparison of murine and human microarray data

[Matthew McCall]

Bas,

My (biased) recommendation would be fRMA + barcode. Comparing human
and mouse microarray data is Figure 2 of the barcode paper:
http://nar.oxfordjournals.org/content/39/suppl_1/D1011.full

You still need to be careful with the orthologous gene mapping.

Best,
Matt


On Tue, Apr 22, 2014 at 10:22 AM, Sylvain Brohée <sbrohee at ulb.ac.be> wrote:
> Hi Bas,
>
> First of all, I would say that I would not recommend to to this kind of
> stuff as it seems kind of dirty to me.
>
> However, recently, I was 'kindly' asked to perform this type of analyze and
> I used the good old ComBat function from the sva package to remove the batch
> effect between human and mouse. In order to have a reliable matrix from the
> beginning, I used only those genes that had the same gene names (in capital
> letters for mouse).
>
> This is the code I used :
>
> Let's eset be the mouse dataset and human.exp.names.agg be the human
> dataset. Genes are in rows and experiments in columns.
>
> row.names(eset) <- toupper(row.names(eset))
> human.mouse.complete <- merge(human.exp.names.agg, eset, by = 'row.names')
> row.names(human.mouse.complete) <- human.mouse.complete[,1]
> human.mouse.complete <- human.mouse.complete[,-1]
> pheno.mod0 <- data.frame(row.names = names(human.mouse.complete), fact.1 =
> rep(1, ncol(human.mouse.complete)), fact.2 =  rep(2,
> ncol(human.mouse.complete)))
> mod0 <- model.matrix(~1, data = pheno.mod0)
> human.mouse.complete.combat <- ComBat(human.mouse.complete, c(rep(1,
> human.exp.nb), c(rep(2,22))), mod = mod0)
>
> It seemed to give satisfactory results.
>
> If there are more "clever" ways, I would be happy to hear about them!
>
> Cheers,
>
> Sylvain
>
>
>
> On 04/22/2014 04:04 PM, Bas van Gestel wrote:
>>
>> Dear all,
>> For a project I would like to compare the gene expression of different
>> immune cells in both mouse and human. For the immune cells of interest,
>> microarray data is available. The microarray data for the human immune cells
>> have been generated with the same platform. The microarray data for the
>> murine immune cells have been generated with the same platform, although
>> with a different platform than used for the human immune cells. I performed
>> RMA normalization using the rma function in the affy package separately for
>> the human and the murine datasets. However, I would like to compare the gene
>> expression levels of mouse and human immune cells. I therefore would like to
>> ask you the following questions:What is the recommended way to normalize the
>> RMA normalized datasets of human and mouse, so that I can compare/combine
>> both datasets?
>> Thanks a lot for your help.
>> Kind regards, Bas
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> 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



-- 
Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880