User: user31888

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user3188830
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New User
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United States
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2 weeks, 6 days ago
Joined:
2 years, 7 months ago
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Posts by user31888

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Using DESeq2 normalisation method on a tximport list of matrices without sample
... Thanks for your explanation ! ...
written 20 days ago by user3188830
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Comment: C: How to obtain a normalised expression matrix from read counts and scaling factor
... Ok, I see. Thanks Ryan ! ...
written 24 days ago by user3188830
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Comment: C: How to obtain a normalised expression matrix from read counts and scaling factor
... Thanks Ryan. The only way I see I could use the cpm function would be as follows: > cpm(matrix, normalized.lib.sizes=F, weights=upQuartileFactors)         sample1   sample2   sample3 gene1 513117.75 524502.97 538365.03 gene2  37675.41  26919.21  34682.31 gene3 449206.83 448577.82 426952.65 Is ...
written 24 days ago by user3188830
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How to obtain a normalised expression matrix from read counts and scaling factors
... I am trying to get normalised RNASeq expression matrices using different methods. I have a read count matrix: > matrix sample1 sample2 sample3 gene1 13456 16172 13303 gene2 988 830 857 gene3 11780 13831 10550 And I calculated scaling factors w ...
edger written 25 days ago by user3188830 • updated 25 days ago by Ryan C. Thompson6.8k
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Using DESeq2 normalisation method on a tximport list of matrices without sample information
...   From the DESeq2 vignette: txi <- tximport(files, type="salmon", tx2gene=tx2gene) ddsTxi <- DESeqDataSetFromTximport(countData = txi, colData = samples, design = ~ condition) Q1. Is it possible to normalise a gene expression matrix (produced by Salmon and tximport) using DESeq2 method wi ...
deseq2 written 26 days ago by user3188830 • updated 21 days ago by Wolfgang Huber13k
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Comment: C: Create Ensembl transcript to gene IDs table with R ensembldb package for tximpor
... Awesome, thanks Jo ! ...
written 26 days ago by user3188830
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Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
... Following this tutorial, I generated transcript counts with Salmon, but now I'm stuck at the step of building a data frame transcripts to gene IDs (tx2gene) using ensembldb package (for mouse). • Question 1: Using the ensembl package, how one could list the different database versions that exist f ...
salmon ensembldb tximport written 4 weeks ago by user3188830 • updated 4 weeks ago by Johannes Rainer1.3k
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VIPER (Protein Activity Inference) gene expression signature format
... Can we run VIPER (described here) with gene expression signatures generated from RNASeq-based differential expression experiments (e.g. DESeq, EdgeR, ...) instead of microarray data? VIPER manual mentions "It can also take two matrixes as arguments, the first one containing the ‘test’ samples and t ...
viper aracne.networks written 16 months ago by user3188830
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GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
... Hi, Being new to R, I am following the protocol for GAGE from DESeq in the GAGE vignette, but I don't think it fits the setup of my experiment. My read count table is as follow: REF SAMP1 SAMP2 SAMP3 ENSG00000000001.6 0 1 1 4 ENSG00000000008.3 1 6 3 ...
deseq gage pathview written 16 months ago by user3188830
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Comment: C: GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
... I tried that, but it returned the same error. Anyway, I used the edgeR fork to bypass the 'exp.d' calculation and it works now. Thanks ! ...
written 18 months ago by user3188830

Latest awards to user31888

Popular Question 16 months ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Popular Question 16 months ago, created a question with more than 1,000 views. For Pathview: *** caught segfault *** cause 'memory not mapped'
Popular Question 16 months ago, created a question with more than 1,000 views. For Pathview: *** caught segfault *** cause 'memory not mapped'

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