User: relathman

gravatar for relathman
relathman0
Reputation:
0
Status:
New User
Location:
Germany
Last seen:
1 day, 4 hours ago
Joined:
1 year, 10 months ago
Email:
r***************@charite.de

Posts by relathman

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answers
64
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 8 days ago by relathman0
2
votes
1
answer
64
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 9 days ago by relathman0 • updated 9 days ago by Michael Love18k
0
votes
1
answers
293
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 10 months ago by relathman0
1
vote
1
answer
293
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 10 months ago by relathman0 • updated 10 months ago by James W. MacDonald46k
0
votes
1
answers
455
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 10 months ago by relathman0
0
votes
1
answer
455
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 11 months ago by relathman0 • updated 10 months ago by James W. MacDonald46k
0
votes
1
answers
586
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 11 months ago by relathman0
0
votes
1
answer
226
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 12 months ago by relathman0 • updated 12 months ago by James W. MacDonald46k
0
votes
0
answers
189
views
0
answers
segfault when trying to convert hta20_Hs_ENSE_22.cdf to binary format
... Hi, I want to convert a HTA 2.0 CDF file in ASCII format to binary using affxparser::convertCdf() but run into repeated problems. I have been trying this for hta20_Hs_ENSE_22.cdf (released on Jun 21, 2017) as well as for hta20_hs_ENSE_21.cdf (released on Nov 28, 2016) and the respective ENSG fil ...
cdf affxparser hta2.0 written 12 months ago by relathman0
4
votes
1
answer
428
views
1
answer
How to deal with Affymetrix GeneChip probeids that map to multiple genes
... I am currently working with HTA 2.0 chips (GeneChip® Human Transcriptome Array 2.0). After normalization of the data with RMA, I get 70523 features which I need to annotate for the downstream analysis that includes differential expression and gene enrichment steps. I would like to assign only one ki ...
annotation annotationdbi pd.hta.2.0 hta20sttranscriptcluster.db probe mapping written 22 months ago by relathman0 • updated 22 months ago by James W. MacDonald46k

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: 289 users visited in the last hour