User: Ina Hoeschele

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Ina Hoeschele610
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Posts by Ina Hoeschele

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Rsubread align for miRNAseq?
... Correction to the 2nd half of my first email: I have noticed one potential problem with Rsubread featureCounts function when applied to miRNAseq: When I use the annotation file from mirBase (hsa.gff3) instead of the built-in annotation or the ensembl GTF file, then the Gene IDs in the counts (rowna ...
written 16 months ago by Ina Hoeschele610
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Rsubread align for miRNAseq?
... Hi, For micro RNA (miRNA) data, the following aligners are recommended specifically for these short sequences:     MicroRazerS (www.seqan.de/projects/microrazers/)     mrFAST (mrfast.sourceforge.net/)     mrsFAST (mrsfast.sourceforge.net/Home)     PatMaN (bioinf.eva.mpg.de/patman/) Does anyone know ...
mirna rsubread written 16 months ago by Ina Hoeschele610 • updated 16 months ago by Wei Shi2.7k
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Comment: C: tagwise parameters for negative binomial distribution in edgeR
... Hi Mark, how would the presence of observation outliers potentially causing dispersion outliers be handled in voom? Many thanks, Ina ----- Original Message ----- From: "Mark Robinson" To: "Davide Cittaro" Cc: "Bioconductor mailing list" , "xiaobei.zhou at uzh.ch Zhou" , "Gordon Smyth" Sent: T ...
written 3.9 years ago by Ina Hoeschele610
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Comment: C: voom
... thanks, Wolfgang, I realize that. I did not have time yesterday but will do some more investigating myself today and if nothing shows up I will provide code etc.. Ina ----- Original Message ----- From: "Wolfgang Huber" To: "Ina Hoeschele" Cc: "bioconductor" , "Bioconductor mailing list" Sent: Fr ...
written 4.6 years ago by Ina Hoeschele610
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Comment: C: voom
... thanks, Wolfgang, I realize that. I did not have time yesterday but will do some more investigating myself today and if nothing shows up I will provide code etc.. Ina ----- Original Message ----- From: "Wolfgang Huber" To: "Ina Hoeschele" Cc: "bioconductor" , "Bioconductor mailing list" Sent: Fr ...
written 4.6 years ago by Ina Hoeschele610
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Answer: A: voom
... Hi, I'm using limma's voom function on a (human) RNAseq dataset (regular transcript based count matrix). When I do an MDS plot on the input count matrix, all looks "normal". When I do the same plot on the output log CPM matrix (E), the samples (N=329) cluster strongly into two groups of about equa ...
written 4.6 years ago by Ina Hoeschele610
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voom
... Hi, I'm using limma's voom function on a (human) RNAseq dataset (regular transcript based count matrix). When I do an MDS plot on the input count matrix, all looks "normal". When I do the same plot on the output log CPM matrix (E), the samples (N=329) cluster strongly into two groups of about equa ...
rnaseq written 4.6 years ago by Ina Hoeschele610
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SNP annotation in R
... Hi, I am interested in annotating lists of SNPs in R, mostly I am interested in finding the gene a SNP is located in and for intergenic SNPs which genes are close by. I found this code that wsa developed with the help of Valerie Obenchain: http://adairama.wordpress.com/2013/02/15/functionally-anno ...
snp written 4.7 years ago by Ina Hoeschele610
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Answer: A: SNP annotation in R
... Hi, I am interested in annotating lists of SNPs in R, mostly I am interested in finding the gene a SNP is located in and for intergenic SNPs which genes are close by. I found this code that wsa developed with the help of Valerie Obenchain: http://adairama.wordpress.com/2013/02/15/functionally-anno ...
written 4.7 years ago by Ina Hoeschele610
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Answer: A: problem installing limma
... sorry please forget previous post - I fixed it ... ----- Original Message ----- From: "Ina Hoeschele" To: "bioconductor" , "bioconductor" Sent: Thursday, May 23, 2013 1:49:29 PM Subject: [BioC] problem installing limma Hi, when I try to install limma, I get the error message below. Can someone p ...
written 4.8 years ago by Ina Hoeschele610

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