User: n.kreim

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n.kreim20
Reputation:
20
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New User
Location:
Germany
Last seen:
3 years, 3 months ago
Joined:
4 years, 9 months ago
Email:
n******@imb-mainz.de

Posts by n.kreim

<prev • 10 results • page 1 of 1 • next >
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Answer: A: clusterProfiler: enrichDavid produces NA values
... Hi Guangchuang, Thank you. this explains why the numbers do not match. The numbers do match up if I filter for the padjust. Then the amount of NAs rows matches the amount of rows which are filtered out. I would be great  the information that the filtering is done for adjusted p values to the docu ...
written 3.3 years ago by n.kreim20
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clusterProfiler: enrichDavid produces NA values
... Hi, I have an issue using the enrichDavid function for clusterProfiler. It returns a NA values if there is a pvalue cutoff or a qvalue cutoff. david = enrichDAVID(gene=david.genes, idType="ENTREZ_GENE_ID", minGSSize=3, listType="Gene", annotation="GOTE ...
clusterprofiler written 3.3 years ago by n.kreim20
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Answer: A: Annotation within ChIPSeeker mismatch geneId and annotation column
... Hi Yu,   thanks for the fast answer. It would be great to mention in the description of the function (annotatePeak) that the gene reported is not the nearest gene but the gene with the nearest TSS. In my example the peak is contained within a gene which should be the nearest but is not reported a ...
written 4.1 years ago by n.kreim20
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Annotation within ChIPSeeker mismatch geneId and annotation column
... Hi, I am trying to annotate some peaks from a RIP seq experiment. They are supposed to overlap annotated genes. My problem is that the assigned gene in ChIPSeeker for some of my peaks does not match the gene which is annotated in the annotation column of the returned csAnno object and which is act ...
chipseeker written 4.1 years ago by n.kreim20
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Answer: A: Undefined log2Foldchanges within DEXSeq for significantly regulated exons
... Hi all, Alejandro told me he fixed the issues within the svn repository for release version 1.12.2 and the devel version 1.13.6. So thanks again for the fast fix Alejandro. Nastasja ...
written 4.8 years ago by n.kreim20
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Comment: C: Undefined log2Foldchanges within DEXSeq for significantly regulated exons
... Hi Alejandro, since the data is unpublished I have to talk to the responsible person and come back to you. I may be able to reproduce it with some other already published data. Nastasja ...
written 4.8 years ago by n.kreim20
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Comment: C: Undefined log2Foldchanges within DEXSeq for significantly regulated exons
... Hi Alejandro, I just noticed that the genes which do not have foldchanges assigned to one exon which has a padj value tend to have more than one exon which does not have a padj. The gene I had a look at has 7 exons. Nastasja ...
written 4.8 years ago by n.kreim20
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Answer: A: Undefined log2Foldchanges within DEXSeq for significantly regulated exons
... Hi Alejandro, I was not using the development version but added the changes which were within the two functions estimateExonFoldChanges and fitAndArrangeCoefs to the released Bioconductor version. I do not know if this was clear in the post before. The maxMf parameter is used within the geteffects ...
written 4.8 years ago by n.kreim20
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Answer: A: Undefined log2Foldchanges within DEXSeq for significantly regulated exons
... Hi Alejandro,   thanks for the answer I will check out the changes. I found the maxMf parameter in another post and tried it out. But it did not change anything. Even when increasing it to 150,000. That was when I started to have a look at it. In my case the genes which do not have a log2foldcha ...
written 4.8 years ago by n.kreim20
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Undefined log2Foldchanges within DEXSeq for significantly regulated exons
... While running DEXSeq2 on a Drosophila dataset in triplicates I noticed that some of my differentially regulated exons within my DEXSeqResults object (FDR < 0.05)  have an undefined estimated foldchange but do have an adjusted p-value and associated counts. They also do not have estimated exon coe ...
dexseq written 4.8 years ago by n.kreim20

Latest awards to n.kreim

Popular Question 3.3 years ago, created a question with more than 1,000 views. For Undefined log2Foldchanges within DEXSeq for significantly regulated exons
Scholar 4.8 years ago, created an answer that has been accepted. For A: Undefined log2Foldchanges within DEXSeq for significantly regulated exons

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