User: relathman

gravatar for relathman
relathman0
Reputation:
0
Status:
New User
Location:
Germany
Last seen:
2 months ago
Joined:
2 years ago
Email:
r***************@charite.de

Posts by relathman

<prev • 12 results • page 1 of 2 • next >
0
votes
1
answers
138
views
1
answers
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 9 weeks ago by relathman0
0
votes
1
answers
138
views
1
answers
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 9 weeks ago by relathman0
0
votes
1
answers
138
views
1
answers
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 11 weeks ago by relathman0
2
votes
1
answer
138
views
1
answer
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 11 weeks ago by relathman0 • updated 11 weeks ago by Michael Love19k
0
votes
1
answers
336
views
1
answers
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 12 months ago by relathman0
1
vote
1
answer
336
views
1
answer
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 12 months ago by relathman0 • updated 12 months ago by James W. MacDonald47k
0
votes
1
answers
492
views
1
answers
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 13 months ago by relathman0
0
votes
1
answer
492
views
1
answer
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 13 months ago by relathman0 • updated 13 months ago by James W. MacDonald47k
0
votes
1
answers
703
views
1
answers
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 13 months ago by relathman0
0
votes
1
answer
270
views
1
answer
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 15 months ago by relathman0 • updated 15 months ago by James W. MacDonald47k

Latest awards to relathman

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 219 users visited in the last hour