Normalised data usage

[faraz89]

Hi,

Can the normalised data processed by RUVseq be imported into nSolver Advanced Analysis suite for further downstream analysis?

Faraz

[bhattacharya-a-bt]

I'm not quite sure about this - I don't use the nSolver suite for downstream analyses. I'm pretty sure that the transcriptomic analyses you'll want to run on RUVseq-normalized expression data can be conducted in R.

Arjun Bhattacharya, PhD Postdoctoral Fellow Department of Pathology and Laboratory Medicine Computational Medicine Institute for Quantitative and Computational Biosciences David Geffen School of Medicine University of California, Los Angeles

On Thu, Jun 30, 2022 at 12:52 PM Faraz Khan @.***> wrote:

Hi,

Can the normalised data processed by RUVseq be imported into nSolver Advanced Analysis suite for further downstream analysis?

Faraz

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[faraz89]

Thanks. Just out of curiosity. What R package(es) you use for downstream analysis (DE,GSA,Fusion,SNV)?

best, F

[bhattacharya-a-bt]

I would use either limma or DESeq2 for differential expression, clusterProfiler for GSA. I'm not sure what you mean by Fusion or SNV? Are you trying to call variants from Nanostring data?

On Thu, Jun 30, 2022 at 2:23 PM Faraz Khan @.***> wrote:

Thanks. Just out of curiosity. What R package(es) you use for downstream analysis (DE,GSA,Fusion,SNV)?

best, F

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[faraz89]

Right. So you are using the same packages that are used for NGS RNA-seq data. Fair enough. Thanks.

Yes I meant SNV analysis for nanostring data.

[bhattacharya-a-bt]

Again - not totally sure what you mean by SNV analysis for Nanostring data: Do you mean eQTL analysis or calling genotypes from Nanostring data? The latter is not possible since you don't have a sequence.

On Thu, Jun 30, 2022 at 2:37 PM Faraz Khan @.***> wrote:

Right. So you are using the same packages that are used for NGS RNA-seq data. Fair enough. Thanks.

Yes I meant SNV analysis for nanostring data.

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[faraz89]

Please see attached screenshot for the type of analysis I was talking about.

[bhattacharya-a-bt]

I'm not familiar with this unfortunately - I've only dealt with the RNA expression data from NanoString.

On Thu, Jun 30, 2022 at 3:05 PM Faraz Khan @.***> wrote:

[image: Screenshot 2022-06-30 at 18 03 43] https://user-images.githubusercontent.com/24622959/176786595-f3ca6899-4c31-4081-afb6-6ed966f8cb5b.png

Please see attached screenshot for the type of analysis I was talking about.

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