User: relathman

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relathman0
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Posts by relathman

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Comment: C: Transcript abundance estimation for time-course RNA-seq data
... Thanks a lot! Would tpm.mat then be the matrix of the originally estimated transcript counts (unscaled TPMs = countsFromAbundance="no" option from tximport) as output by Salmon? ...
written 14 months ago by relathman0
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Comment: C: Transcript abundance estimation for time-course RNA-seq data
... I've followed your advice and used tximport for read depth normalization of the Salmon TPM values. In the next step, I want to normalize between samples using TMM from edgeR. I am not necessarily interested in performing classical DTU/DGE analysis but rather want to visualize and compare the express ...
written 14 months ago by relathman0
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Comment: C: Transcript abundance estimation for time-course RNA-seq data
... Many thanks for your fast reply and your explanation. Since Salmon can either map reads itself as well as work with precomputed read alignments, I am unsure what the best approach would be - does quantification with Salmon work "better" with Salmon-mapped reads or are these two independent steps? ...
written 14 months ago by relathman0
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Transcript abundance estimation for time-course RNA-seq data
... Dear community, I am currently analysing a set of time-course (~10 time points) stranded paired-end RNA-seq data with the particular objective of identifying time-dependent changes in alternative splicing. However, I am still undecided whether alpine or Salmon or another method would be better sui ...
rna-seq salmon alpine transcript expression written 14 months ago by relathman0 • updated 14 months ago by Michael Love25k
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Comment: C: Use of RMA to get exon-level summaries for HTA 2.0
... Thank you very much for your fast and helpful response. I would have liked to find some of my top candidates for alternatively spliced genes from the FIRMA analysis in the diffSplice results as well without judging the quality of the methods themselves. I assume that as long as we don’t know the id ...
written 2.0 years ago by relathman0
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Use of RMA to get exon-level summaries for HTA 2.0
... Dear community, is it possible to use RMA to get exon-level summaries for the HTA 2.0 platform in Bioconductor? I would like to run diffSplice() from limma to detect genes that have evidence for differential splicing between two conditions and I need an expression matrix with counts at the exon lev ...
annotation exon array analysis differential exon usage diffsplice hta2.0 written 2.0 years ago by relathman0 • updated 2.0 years ago by James W. MacDonald51k
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Comment: C: Filtering of lowly expressed probes in HTA 2.0 using new pd.hta.2.0 version 3.12
... Great, it works now! Thank you very much for your help. ...
written 2.1 years ago by relathman0
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Filtering of lowly expressed probes in HTA 2.0 using new pd.hta.2.0 version 3.12.2
... Dear Community, as described in this post (https://support.bioconductor.org/p/94554/#94571), I would like to plot the distribution for main, antigenomic and intronic probesets in an HTA 2.0 in order to decide on an appropriate expression cutoff to separate expressed from unexpressed probesets. Acc ...
affycoretools pd.hta.2.0 hta2.0 written 2.1 years ago by relathman0 • updated 2.1 years ago by James W. MacDonald51k
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Comment: C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
... Thank you very much for your explanation on why paCalls does not work for HTAFeatureSets and for describing an alternative method on how to find an appropriate cutoff to separate expressed from unexpressed probesets. I am working with HTA 2.0 as well and tried to follow your advice of simply plotti ...
written 2.1 years ago by relathman0
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Time-course analysis with limma for >3 time points
... Dear all, I want to use limma for the analysis of changing values over time. My data set consists of 2 conditions and 9 evenly spread time points (without replicates) for each condition. I have two biological questions that I would like to address: 1)    I want to identify genes whose values change ...
timecourse limma design matrix multiple time points contrast matrix written 2.2 years ago by relathman0 • updated 2.2 years ago by James W. MacDonald51k

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