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Question: BiSeq trimClusters FDR.loc confusion
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gravatar for mnaymik
2.6 years ago by
mnaymik10
United States
mnaymik10 wrote:

Hi I am running the BiSeq software and have 2 rejected clusters after running testClusters with FDR.cluster=0.1

When I attempt to run trimClusters on these two clusters I get no results unless I use a FDR.loc >= 1.5... I am having some trouble understanding what exactly this FDR.loc number means, in general and one as high as 1.5, and also why I have to use one so high to even see results? Could someone help me with some insight?

 

Thanks,

Marcus

ADD COMMENTlink modified 2.5 years ago • written 2.6 years ago by mnaymik10
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gravatar for mnaymik
2.6 years ago by
mnaymik10
United States
mnaymik10 wrote:

Hi Katja,

Sorry one more question. Is there a way to write the DMRs object to a csv?

 

Thanks,

Marcus

ADD COMMENTlink written 2.6 years ago by mnaymik10
If your DMRs are GRanges do yourDMRs <- as.data.frame(DMR.GRanges) and then: write.table(yourDMRs, file = "yourDMRs.csv", rownames = FALSE, quote = FALSE, sep = "\t") Cheers, Katja ----- Original Message ----- > From: "mnaymik [bioc]" <noreply@bioconductor.org> > To: katjah@stanford.edu > Sent: Monday, April 27, 2015 10:09:18 AM > Subject: [bioc] A: BiSeq trimClusters FDR.loc confusion > Activity on a post you are following on support.bioconductor.org > User mnaymik wrote Answer: BiSeq trimClusters FDR.loc confusion : > Hi Katja, > Sorry one more question. Is there a way to write the DMRs object to a csv? > Thanks, > Marcus > You may reply via email or visit > A: BiSeq trimClusters FDR.loc confusion
ADD REPLYlink written 2.6 years ago by Katja Hebestreit110
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gravatar for Katja Hebestreit
2.6 years ago by
United States
Katja Hebestreit110 wrote:

Hi Marcus,

Are you sure that you used an FDR.loc > 1? What other values for FDR.loc did you try?

In general, it can happen that testing on CpG-wise level with the same FDR that you used for calling significant regions doesn't result in any significant CpG sites.

Cheers,

Katja

ADD COMMENTlink written 2.6 years ago by Katja Hebestreit110
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gravatar for mnaymik
2.6 years ago by
mnaymik10
United States
mnaymik10 wrote:

Yes, I tried incrementing the fdr.loc from .1 up to 1.5 by .1 until the results were not null. The way the code is written you are not restricted to any value <1. I tried 10 and got more locations than at 1.5. I imagine using something like 1000000 would just spit out every bp that was in the range of the cluster. This is why I am confused because statistically it seems that 1 should be the highest.

ADD COMMENTlink written 2.6 years ago by mnaymik10
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gravatar for Katja Hebestreit
2.6 years ago by
United States
Katja Hebestreit110 wrote:

That is true, the FDR.loc should be restricted to be between 0 and 1. I will change this.

To figure out the problem here I would need reproducible data. Would it be possible for you to send me a subset of your data (e.g. only one chromosome) together with your code?

ADD COMMENTlink written 2.6 years ago by Katja Hebestreit110
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gravatar for mnaymik
2.6 years ago by
mnaymik10
United States
mnaymik10 wrote:

Yes, how should I send it? 

ADD COMMENTlink written 2.6 years ago by mnaymik10
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gravatar for mnaymik
2.6 years ago by
mnaymik10
United States
mnaymik10 wrote:

I uploaded the .r script and chr 3 of the data, .bedgraph and .cov files, compressed into a tar.gz to my github @ https://github.com/naymikm/BiSeq_subset

Thank you very much!

Marcus

ADD COMMENTlink written 2.6 years ago by mnaymik10
1
Okay, thank you! I will look into it and will let you know! Cheers, Katja ----- Original Message ----- > From: "mnaymik [bioc]" <noreply@bioconductor.org> > To: katjah@stanford.edu > Sent: Thursday, April 16, 2015 10:06:51 AM > Subject: [bioc] A: BiSeq trimClusters FDR.loc confusion > Activity on a post you are following on support.bioconductor.org > User mnaymik wrote Answer: BiSeq trimClusters FDR.loc confusion : > I uploaded the .r script and chr 3 of the data, .bedgraph and .cov files, > compressed into a tar.gz to my github @ > https://github.com/naymikm/BiSeq_subset > Thank you very much! > Marcus > You may reply via email or visit > A: BiSeq trimClusters FDR.loc confusion
ADD REPLYlink written 2.6 years ago by Katja Hebestreit110
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gravatar for mnaymik
2.6 years ago by
mnaymik10
United States
mnaymik10 wrote:

Hi Katja,

I figured out the issue. There was a problem with 2 of the samples that we decided to ultimately throw out due to sequencing quality issues, without these two samples the analysis runs fine. I do have one trivial question though just to be 100% sure... In the DMR results group 1 and group 2 correspond to the same order as the levels of factor(colData(rrbs)$group)?  In my case factor(colData(rrbs)$group) shows: 

Levels: L O

Hence, L is group 1 and O is group 2?

Thanks again,

Marcus

ADD COMMENTlink written 2.6 years ago by mnaymik10
Hi Marcus, Yes, exactly, the groups 1 and 2 correspond to the same order as the levels of the group factor. It's good that you don't run into this problem anymore. If you don't mind, I would still like to use your data to figure out why BiSeq showed this weird behavior. I just haven't had time yet. If you don't delete the files from Github before tomorrow I would still like to download them. Would that be okay for you? Cheers, Katja ----- Original Message ----- > From: "mnaymik [bioc]" <noreply@bioconductor.org> > To: katjah@stanford.edu > Sent: Wednesday, April 22, 2015 8:48:59 PM > Subject: [bioc] A: BiSeq trimClusters FDR.loc confusion > Activity on a post you are following on support.bioconductor.org > User mnaymik wrote Answer: BiSeq trimClusters FDR.loc confusion : > Hi Katja, > I figured out the issue. There was a problem with 2 of the samples that we > decided to ultimately throw out due to sequencing quality issues, without > these two samples the analysis runs fine. I do have one trivial question > though just to be 100% sure... In the DMR results group 1 and group 2 > correspond to the same order as the levels of factor(colData(rrbs)$group)? > In my case factor(colData(rrbs)$group) shows: > Levels: L O > Hence, L is group 1 and O is group 2? > Thanks again, > Marcus > You may reply via email or visit > A: BiSeq trimClusters FDR.loc confusion
ADD REPLYlink written 2.6 years ago by Katja Hebestreit110
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gravatar for mnaymik
2.6 years ago by
mnaymik10
United States
mnaymik10 wrote:

Hi Katja,

Awesome thank you! Yes that is fine, I will leave them there for a while. To clarify, in the dataset we decided to throw out the samples T01 and  T07 which left 11 samples of L (control) and 9 samples of O (case).

Thanks,

Marcus

ADD COMMENTlink written 2.6 years ago by mnaymik10
Great! Thanks a lot! Katja ----- Original Message ----- > From: "mnaymik [bioc]" <noreply@bioconductor.org> > To: katjah@stanford.edu > Sent: Thursday, April 23, 2015 9:35:11 AM > Subject: [bioc] A: BiSeq trimClusters FDR.loc confusion > Activity on a post you are following on support.bioconductor.org > User mnaymik wrote Answer: BiSeq trimClusters FDR.loc confusion : > Hi Katja, > Awesome thank you! Yes that is fine, I will leave them there for a while. To > clarify, in the dataset we decided to throw out the samples T01 and T07 > which left 11 samples of L (control) and 9 samples of O (case). > Thanks, > Marcus > You may reply via email or visit > A: BiSeq trimClusters FDR.loc confusion
ADD REPLYlink written 2.6 years ago by Katja Hebestreit110
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gravatar for mnaymik
2.5 years ago by
mnaymik10
United States
mnaymik10 wrote:

Hi Katja,

Another question, I wanted to clarify what the median.p value is. Is this the median p-value for all sites within each DMR from the Wald test when testing for group effect?

Thanks,

Marcus

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by mnaymik10
Hi Marcus, Exactly, median.p is the median of all p-values arising from the CpG-wise Wald tests for group comparison. Cheers, Katja ----- Original Message ----- > From: "mnaymik [bioc]" <noreply@bioconductor.org> > To: katjah@stanford.edu > Sent: Monday, May 18, 2015 1:15:57 PM > Subject: [bioc] A: BiSeq trimClusters FDR.loc confusion > Activity on a post you are following on support.bioconductor.org > User mnaymik wrote Answer: BiSeq trimClusters FDR.loc confusion : > Hi Katja, > Another question, What exactly is the median.p value that is in the DMR > object refer to? I have been assuming that this is the p-value that was from > the Wald test when testing for group effect is this correct? > Thanks, > Marcus > You may reply via email or visit > A: BiSeq trimClusters FDR.loc confusion
ADD REPLYlink written 2.5 years ago by Katja Hebestreit110
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