Question: MethylKit DSS Package
0
gravatar for nilaycan
10 months ago by
nilaycan0
nilaycan0 wrote:

Dear Sir/Madam,

I have tried Methylkit with many datasets and it always worked well using the function calculateDiffMethDSS.

However, I am trying to run a data set with no replicates and it crashed when running calculateDiffMethDSS. It returns the error:

Error in rowMeans(p) : 'x' must be an array of at least two dimensions

The same data set works well using calculateDiffMeth instead of calculateDiffMethDSS.

Do you have any ideas why? Could it be because that there are no replicates?


Please, let me know if you need more information.

 

Best Regards,

Nilay Can
 

ADD COMMENTlink modified 10 months ago by altuna akalin20 • written 10 months ago by nilaycan0
Answer: MethylKit DSS Package
0
gravatar for altuna akalin
10 months ago by
Germany/Berlin/MDC-BIMSB
altuna akalin20 wrote:
Yes, this is because there are no replicates. calculateDiffMeth will run just the fisher’s exact test when there no replicates. That’s why it works when there are no replicates On Tue 17. Jul 2018 at 17:13, nilaycan [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User nilaycan <https: support.bioconductor.org="" u="" 16507=""/> wrote Question: > MethylKit DSS Package <https: support.bioconductor.org="" p="" 111089=""/>: > > Dear Sir/Madam, > > I have tried Methylkit with many datasets and it always worked well using > the function calculateDiffMethDSS. > > However, I am trying to run a data set with no replicates and it crashed > when running calculateDiffMethDSS. It returns the error: > > Error in rowMeans(p) : 'x' must be an array of at least two dimensions > > The same data set works well using calculateDiffMeth instead of > calculateDiffMethDSS. > > Do you have any ideas why? Could it be because that there are no > replicates? > > > Please, let me know if you need more information. > > > > Best Regards, > > Nilay Can > > > ------------------------------ > > Post tags: R, bioconductor, methylation, methylkit > > You may reply via email or visit > MethylKit DSS Package > -- Sent from mobile, excuse the brevity
ADD COMMENTlink written 10 months ago by altuna akalin20

Dear Akalin,

Thanks for your response. 

Best Regards,

Nilay

ADD REPLYlink written 10 months ago by nilaycan0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 226 users visited in the last hour