[BioC] Comparison of murine and human microarray data

[Steve Piccolo]

Ying,

You might also consider trying the SCAN.UPC package for this. It can
normalize both types of microarrays, and it now has the ability to
integrate with the ComBat function of the sva package.

Regards,
-Steve


>>On Tue, Apr 22, 2014 at 10:22 AM, Sylvain Broh?e <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]]
>>>>
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>>>
>>>
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>>--
>>Matthew N McCall, PhD
>>112 Arvine Heights
>>Rochester, NY 14611
>>Cell: 202-222-5880
>>_______________________________________________
>>Bioconductor mailing list
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