MEDIPS: case study with different replicate numbers of control and case
1
0
Entering edit mode
fmhsu0114 • 0
@fmhsu0114-12157
Last seen 4.8 years ago

Dear all,

I'm using MEDIPS to process MBD-seq data, with 2 control replicates and 3 case replicates. It seems that the MEDIPS.meth function needs same length of MSet (I got error message 'MEDIPSset/MEDIPSroiSet objects are of different length').  Any advice for this issue? I can use the MEDIPS.mergeSets, but this will make the replicates into one.

Thanks in advance,

Fei

MEDIPS • 631 views
ADD COMMENT
0
Entering edit mode
Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 3.7 years ago
USA/La Jolla/UCSD
Dear Fei, comparisons of groups with different numbers of samples should not be a problem. You are referring to a different number of genomic regions tested for. Please create MEDIPS SETs or MEDIPSroiSets with the same parameter settings so that the resulting coverage vectors have the same length. Combining a MEDIPS SET for e.g. 500bp windows genome wide with a MEDIPSroiSet created for e.g. promoter regions only, is not possible. I hope this helps. All the best, Lukas On 12 Jan 2017, at 10:41, fmhsu0114 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User fmhsu0114<https: support.bioconductor.org="" u="" 12157=""/> wrote Question: MEDIPS: case study with different replicate numbers of control and case<https: support.bioconductor.org="" p="" 91110=""/>: Dear all, I'm using MEDIPS to process MBD-seq data, with 2 control replicates and 3 case replicates. It seems that the MEDIPS.meth function needs same length of MSet (I got error message 'MEDIPSset/MEDIPSroiSet objects are of different length'). Any advice for this issue? I can use the MEDIPS.mergeSets, but this will make the replicates into one. Thanks in advance, Fei ________________________________ Post tags: MEDIPS You may reply via email or visit MEDIPS: case study with different replicate numbers of control and case
ADD COMMENT

Login before adding your answer.

Traffic: 352 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