User: Ina Hoeschele

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Ina Hoeschele610
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Posts by Ina Hoeschele

<prev • 66 results • page 1 of 7 • next >
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Comment: C: TPM and FPKM for lncRNA
... Update: I just did the same for protein-coding genes using mRNA-seq data and am also getting gene lengths that are shorter than the fragment lengths, so something may be wrong with my gene length calculation? See below. library(GenomicFeatures) txdb <- makeTxDbFromGFF("/home/inah/MESA_mRNAseq_N ...
written 22 days ago by Ina Hoeschele610
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TPM and FPKM for lncRNA
... Hi, I have total RNA-seq data and would like to compute TPM and FPKM values for a read count matrix generated for lncRNAs using the annotation file gencode.v28.long_noncoding_RNAs.gtf. To compute TPM and FPKM from the counts I first need the lengths of the lncRNA genes, which I obtain by summing th ...
genomicfeatures lncrna fpkm tpm written 22 days ago by Ina Hoeschele610
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Comment: C: strange results with featureCounts
... thank you very much for the quick response, Wei.  I have one other question: The percentage of successfully assigned fragments is 52% and 49.4% in these two total RNA samples. Is this unusually low? Thanks again, Ina ...
written 5 weeks ago by Ina Hoeschele610
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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 20 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 20 months ago by Ina Hoeschele610 • updated 20 months ago by Wei Shi2.8k
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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 4.3 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 5.0 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 5.0 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 5.0 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 5.0 years ago by Ina Hoeschele610

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