[Bioc-devel] differential expression tools for proteins

[Diego Morais]

Hi Cardin,
this package does not do the same as DESeq2,
http://bioconductor.org/packages/3.7/bioc/vignettes/transcriptogramer/inst/doc/transcriptogramer.html,
but you can use it to do a differential expression for proteins (case x
control).

2018-01-06 14:45 GMT-03:00 Cardin Julie via Bioc-devel <
bioc-devel at r-project.org>:

> Hi,
>    I have experienced very good results with DESeq2 for my RNASeq
> analysis. As far as I understand, it is a tool that normalise our data from
> sequencing to make them comparable.
>
> I have a new project implicating proteins counts.
> I have  couple of data sets. For each sample we have:
> rows with proteins names (instead of genes), with their respective counts.
>
> My goal is again to make a differential expression between treated groups
> versus controls.
> I wonder if I can use DESeq2 to do a differential expression for proteins?
> Or if the correcting factor that is used by DESeq2 to correct counts for
> RNASeq is specific to DNA sequencing and it is not applicable to proteins?
>
> Is there a tool that do the exact same thing as DESeq2 but for proteins?
>
> Thank you very much for your help and time,
> Best regards and happy new year!
>
> Julie Cardin
> Bioinforamatician
> IRCM
>
>
>
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>
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-- 
Atenciosamente,
Diego Arthur de Azevedo Morais

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