User: relathman

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relathman0
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Germany/Berlin/Charité
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1 year, 2 months ago
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r***************@charite.de

Posts by relathman

<prev • 8 results • page 1 of 1 • next >
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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 10 weeks 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 10 weeks ago by relathman0 • updated 10 weeks ago by James W. MacDonald45k
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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. Would a cutoff of ~2.5 be appropriate for the following sample to filter out most lowly expressed probes? ...
written 12 weeks 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 3 months ago by relathman0 • updated 3 months ago by James W. MacDonald45k
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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 3 months 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 4 months ago by relathman0 • updated 4 months ago by James W. MacDonald45k
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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 5 months ago by relathman0
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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 14 months ago by relathman0 • updated 14 months ago by James W. MacDonald45k

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