MethylKit DSS Package
1
0
Entering edit mode
nilaycan • 0
@nilaycan-16507
Last seen 3.2 years ago

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
 

R bioconductor methylation methylkit • 468 views
ADD COMMENT
0
Entering edit mode
@altuna-akalin-7813
Last seen 2.7 years ago
Germany/Berlin/MDC-BIMSB
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 COMMENT
0
Entering edit mode

Dear Akalin,

Thanks for your response. 

Best Regards,

Nilay

ADD REPLY

Login before adding your answer.

Traffic: 145 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6