Question

FourCSeq- without replicates

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tlgolan • 0

@tlgolan-10804

Last seen 8.3 years ago

Hi,

Does anyone know if I can use FourCSeq on my 4Cseq data in case that my data doesn't contain replicate samples?

Thanks,

Tal

fourcseq • 1.1k views

ADD COMMENT • link updated 8.5 years ago by felix.klein ▴ 150 • written 8.5 years ago by tlgolan • 0

score 0 · Answer 1 · 2016-05-31

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felix.klein ▴ 150

@felixklein-6900

Last seen 6.4 years ago

Germany

Hello Tal, if you have several conditions from one viewpoint you can try to run the pipeline. However it will be hard to tell whether detected differences are due to technical noise or the different conditions. Best regards, Felix On 05/31/2016 08:34 AM, tlgolan [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User tlgolan <https: support.bioconductor.org="" u="" 10804=""/> wrote > Question: FourCSeq- without replicates > <https: support.bioconductor.org="" p="" 83226=""/>: > > Hi, > > Does anyone know if I can use FourCSeq on my 4Cseq data in case that > my data doesn't contain replicate samples? > > Thanks, > > Tal > > ------------------------------------------------------------------------ > > Post tags: fourcseq > > You may reply via email or visit > FourCSeq- without replicates >

ADD COMMENT • link 8.5 years ago felix.klein ▴ 150

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Hello Felix, Is there any way to get the FourCSeq-Pipeline running without any replicates or samples under different conditions? I am setting up 4C-Seq and only have sequencing outputs without replicates so far. I tried doing FourCSeq with one of my sequence files and ran into following error during creation of the FourCobject:

Error in DESeqDataSet(SummarizedExperiment(colData = colData, metadata = metadata, : design has a single variable, with all samples having the same value. use instead a design of '~ 1'. estimateSizeFactors, rlog and the VST can then be used In addition: Warning message: In DESeqDataSet(SummarizedExperiment(colData = colData, metadata = metadata, : all genes have equal values for all samples. will not be able to perform differential analysis

I guess this has to do with singular samples without replicates. Thats why I tried it again (just for fun), this time by just copying one of the bam files and using that as replicate, but then I ran into a similar error when getting Z Scores. Is there any workaround for me or is there simply no way to use FourCSeq without replicates? I know, not having replicates will not generate meaningful data, but I want to see how the output from FourCSeq compares to other algorithms like 4Cker (which worked with singular samples by the way).

Thanks, Johannes

ADD REPLY • link 5.5 years ago johannes.schmidpeter • 0