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itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
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how to use #43

Closed xflicsu closed 8 years ago

xflicsu commented 8 years ago

Hello PORT developer,

 I got the SPREADSHEETS information of genes.

id N1 N2 N3 T1 T2 T3 geneCoordinate geneSymbol gene:ENSMUSG00000000001 22 16 22 29 30 26 chr3:107910198-107949064 Gnai3 gene:ENSMUSG00000000028 0 4 4 0 2 1 chr16:18780540-18812080 Cdc45 gene:ENSMUSG00000000037 3 0 2 0 0 2 chrX:157555125-157696145 Scml2 gene:ENSMUSG00000000049 56 56 58 70 57 66 chr11:108204668-108275710 Apoh gene:ENSMUSG00000000056 259 278 266 110 104 94 chr11:121098567-121117170 Narf

We have two groups of samples. I wonder the whether these values need to be re-normalize to TPM/RPKM. And can I directly input these value to DESeq to identify differential expression? Is it necessary to re-normalize by using DESeq? BTW, is there any tool to convert this value to TPM or RPKM?

greggrant commented 8 years ago

Hi Xianfeng, thanks for your interest in PORT. The answer to your question is "no" once you get the spreadsheet out of PORT no further normalization is necessary. We definitely advise against using the TPM, RPKM or anthing like that. The counts are already fully normalized after PORT. Best Regards, Greg

On Sat, Jun 4, 2016 at 5:28 AM, Xianfeng Li notifications@github.com wrote:

Hello PORT developer,

I got the SPREADSHEETS information of genes.

id N1 N2 N3 T1 T2 T3 geneCoordinate geneSymbol gene:ENSMUSG00000000001 22 16 22 29 30 26 chr3:107910198-107949064 Gnai3 gene:ENSMUSG00000000028 0 4 4 0 2 1 chr16:18780540-18812080 Cdc45 gene:ENSMUSG00000000037 3 0 2 0 0 2 chrX:157555125-157696145 Scml2 gene:ENSMUSG00000000049 56 56 58 70 57 66 chr11:108204668-108275710 Apoh gene:ENSMUSG00000000056 259 278 266 110 104 94 chr11:121098567-121117170 Narf

We have two groups of samples. I wonder the whether these values need to be re-normalize to TPM/RPKM. And can I directly input these value to DESeq to identify differential expression? Is it necessary to re-normalize by using DESeq? BTW, is there any tool to convert this value to TPM or RPKM?

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xflicsu commented 8 years ago

Thanks for you response! It is very useful for my sub-analysis.