If I need to convert my values to RPKM in order to be comparable/consistent
with the public RNAseq RPKM values, then I could compare both RPKM values
directly, not even bother to use UPC values. What do you think?

Many thanks,
Shirley


On Fri, Jun 27, 2014 at 9:14 AM, Steve Piccolo <stephen.piccolo@hsc.utah.edu
> wrote:

>  If possible, I’d suggest converting your values to RPKM for consistency.
> UPC should be robust to these differences. However, I have not evaluated
> this extensively.
>
>
>   From: shirley zhang <shirley0818@gmail.com>
> Date: Friday, June 27, 2014 at 6:59 AM
>
> To: Stephen Piccolo <stephen.piccolo@hsc.utah.edu>
> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
> Subject: Re: SCAN.UPC for microarray and RNAseq data
>
>    Hi Steve,
>
>  Many thanks for your quick response.
>
> For RNAseq data, I have to compare my own RNAseq data with public RNAseq
> data which contains > 3000 samples. For this comparison,
>
> 1. I am planing to try UPC_RNASeq with read.counts as input for my own
> data.
> 2. However, the public large RNAseq data use RKPM value.
>
> Do you think it is reasonable by comparing UPCs generating from different
> type of input values?
>
>  Many thanks,
> Shirley
>
>
>
> On Fri, Jun 27, 2014 at 8:49 AM, Steve Piccolo <
> stephen.piccolo@hsc.utah.edu> wrote:
>
>>  Hi Shirley,
>>
>>  1. We recommend that you use raw RNA-Seq counts as input to UPC_RNASeq.
>> However, you could try using RPKM values and see how it works. My guess is
>> that the results will be comparable, but I have not tested this
>> extensively. In this case, it may not be necessary to correct for gene
>> length, but you may still want to correct for GC content.
>>
>>  2. Yes, in the latest version we added functions called UPC_Generic and
>> UPC_Generic_ExpressionSet that are designed to UPC normalize any type of
>> data, even if it has been pre-normalized. Give that a try and let me know
>> if you have any questions.
>>
>>  -Steve
>>
>>   From: shirley zhang <shirley0818@gmail.com>
>> Date: Friday, June 27, 2014 at 6:08 AM
>> To: Stephen Piccolo <stephen.piccolo@hsc.utah.edu>
>> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
>> Subject: SCAN.UPC for microarray and RNAseq data
>>
>>   Dear Steve,
>>
>> I have a very large Affy Exon array data including >1000 samples, and I
>> would like to compare them with RNAseq data.
>>
>>  1. In the SCAN..vignette.pdf, UPC_RNASeq can take read.counts matrix in
>> which each row is for one gene, and each column for each sample. Is it
>> possilbe for UPC taking RPKM value as input?
>>
>> 2. My exon array data has been preprocessed using RMA, and adjusted for
>> many technical variables. So I have a data matrix with gene-level RMA log2
>> value for each gene across all 1,000 samples. Can I use UPC normalize my
>> data by directly using this data matrix as an input file.
>>
>>  Many thanks,
>> Shirley
>>
>>
>>
>>
>

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