User: Katja Hebestreit

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Posts by Katja Hebestreit

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Comment: C: BiSeq. Model beta regression on resampled data.
... Hi Jose, You could also do this: group 1 with 6 cases and 3 controls and group 2 with 6 cases and 3 controls. As long as you have the same ratio of controls to cases in both groups you should be fine. It's actually better to include a similar number of samples in your resampled data as you use in t ...
written 10 months ago by Katja Hebestreit110
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Answer: A: BiSeq. Model beta regression on resampled data.
... Hi Jose, The additional explanatory variable shouldn't change much for the resampling. If your explanatory variable of interest (group) has 2 values, the two sampled groups should contain the same number of samples with each value. The only thing that is different is that you also need to add gende ...
written 10 months ago by Katja Hebestreit110
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Job: Bioinformatics position at the Department of Genetics, Stanford, California
... Research Data Analyst 1 (Job Number: 70840) Description An exciting opportunity is available for a bioinformatician in the Department of Genetics at Stanford University. The position offers the opportunity to contribute to cutting edge research in the field of aging, in particula ...
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Answer: A: BiSeq trimClusters error
... Hi Manu, I am glad it is working now! The assumption is that the p-values are uniformly distributed under the null hypothesis. This is not always the case in real datasets. For example, the p-values are less well uniformly distributed the viewer samples you have. There can also be a problem with v ...
written 21 months ago by Katja Hebestreit110
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Answer: A: BiSeq trimClusters error
... Hi Manu, I am glad it is working now! The assumption is that the p-values are uniformly distributed under the null hypothesis. This is not always the case in real datasets. For example, the p-values are less well uniformly distributed the viewer samples you have. There can also be a problem with v ...
written 21 months ago by Katja Hebestreit110
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Answer: A: BiSeq trimClusters error
... Hi Manu, Thanks for the figure of the variogram. You can interpret the variogram as 1-correlation, which means it has to be between 0 and 1. For some data the variogram tends goes beyond 1, as it does in your example. In cases like this, you should set your sill to 1: smoothVariogram( vario.Cardpl ...
written 22 months ago by Katja Hebestreit110
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Answer: A: BiSeq trimClusters error
... Hi Manu, Regarding your first question: In a first step BiSeq tests all CpG clusters (= regions of high CpG density) for differential methylation. When a CpG cluster is significant, this doesn't necessarily mean that all CpG sites within this region are differentially methylated. That's why trimClu ...
written 22 months ago by Katja Hebestreit110
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Comment: C: BiSeq trimClusters FDR.loc confusion
... 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 ...
written 2.5 years ago by Katja Hebestreit110
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Comment: C: SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
... Hi Maria, It sounds like you have NAs in your CpGs that are not covered. Please replace the NAs by a 0 in the totalReads and methReads slots. Does that help? Cheers, Katja ----- Original Message ----- > From: "maria.maqueda [bioc]" <noreply@bioconductor.org> > To: katjah@stanford ...
written 2.5 years ago by Katja Hebestreit110
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Answer: A: SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
... Hi Maria, I don't know SAAP-BS, but from the column names I suppose that you are right: totalC corresponds to totalReads and methC and to methReads. CpG sites with very high coverages are to be expected. At least I have never seen an RRBS data set without it. In the BiSeq pipeline it is suggested ...
written 2.6 years ago by Katja Hebestreit110

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