User: RNAseqer

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RNAseqer 140
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Very new to RNAseq, previous experience in genome assembly, phylogenetic analysis, substitution rate analysis etc etc.

Posts by RNAseqer

<prev • 88 results • page 1 of 9 • next >
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Comment: C: Is miarma-Seq being maintained?
... Thank you! I missed that bit. ...
written 7 weeks ago by RNAseqer 140
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Is miarma-Seq being maintained?
... I was wondering if anyone uses miARma-Seq, and is it being maintained/kept up to date? Thanks! https://sourceforge.net/projects/miarma/ ...
miarma-seq rna-seq mirna written 7 weeks ago by RNAseqer 140
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best practices/ pipeline for miRNA sequencing QC
... I'm currently searching the literature for a recent 'best practices' review of miRNA sequencing data QC. I was wondering if there was a pipeline which was A.) well established and B.) widely accepted as rigorous. Looking around there seems to be an 'embarrassment of riches' when looking at QC packag ...
qc mirna-seq rna-seq written 10 weeks ago by RNAseqer 140
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GSEA pvalue output of 0.0. Can I make it more specific?
... I would like to know the exact pvalue Im getting from GSEA. However, GSEA reports a pvalue of 0.0 whenever the value is lower than 1/ # of permutations. The manual recommends upping the number of permutations to get a more specific pvalue, however I would like, if possible, to get the exact pvalue f ...
p-value gsea written 5 months ago by RNAseqer 140
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WGCNA: outputting multiple hubgenes from a module
... I know that WGCNA has the function chooseTopHubInEachModule() to pick the gene with the single highest connectivity within a module, but does it have a function to output several hubgenes from a module? Im looking through the manual and it certainly seems like it should be a straightforward task but ...
hubgenes wgcna written 7 months ago by RNAseqer 140 • updated 7 months ago by Kevin Blighe69k
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constructing a reference matrix from affy 2.0 chip for a 4.0 chip.
... I have some expression for isolated immune cell subsets. I want to use these to make a reference matrix deconvolution. However, this work was done on Affymetrix Multispecies miRNA-1 Array my work was done on miRNA4.0 chips. The expression data is listed on GEO as series GSE28489. Its given identifie ...
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Comment: C: affy Transcriptome Analysis Console (TAC), export expression matrix?
... Just got off the phone with the affy people. Here is how you do this for TAC 4.01: You must do an analysis even if you dont intend to use its output in order to get to the menu option that allows you to export your expression table. So, load in your .cel files using "import cel files in the upper l ...
written 9 months ago by RNAseqer 140
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affy Transcriptome Analysis Console (TAC), export expression matrix?
... Hello everyone, I am starting to work with the Affy Transcription Analysis Console (TAC) on some miRNA4.0 data. I would like to output an expression matrix after RMA normalization/summarization. of the miRNA data. I see from the old Affymetrix Expression Console that there was a way to do this: ...
affy tac expression matrix written 9 months ago by RNAseqer 140
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Is there a good reference matrix for miRNA array deconvolution?
... Hello all, Is there a good miRNA reference matrix for immune cell deconvolution available? Preferably one from non-cancerous cell populations? Id like to get some estimates of immune cell proportions in pd.miRNA.4.0 data. Thanks! ...
deconvolution microarray mirna written 9 months ago by RNAseqer 140 • updated 5 months ago by xinyiy0270
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Small number of genes, drop in sft fit curve at higher threshold powers. why?
... This may be a silly question with an obvious answer, but here goes: I have noticed that when I take my microarray dataset and parse it into smaller chunks (fewer probes/genes per chunk) there is a pattern that appears in my soft fit curve when performing WGCNA. Specifically I get a drop off in the ...
wgcna sft scale-free written 9 months ago by RNAseqer 140 • updated 9 months ago by Kevin Blighe69k

Latest awards to RNAseqer

Popular Question 9 weeks ago, created a question with more than 1,000 views. For No significant DEG: A request to double check my commands for limma.
Popular Question 10 weeks ago, created a question with more than 1,000 views. For No significant DEG: A request to double check my commands for limma.
Popular Question 5 months ago, created a question with more than 1,000 views. For Error "Bioconductor - mirna40cdf not available"
Popular Question 5 months ago, created a question with more than 1,000 views. For pulling snps from vcf file using ids
Popular Question 5 months ago, created a question with more than 1,000 views. For Filtering SNPS by minimum LD value in bcftools?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to in R: Include principal components as covariates in analysis
Popular Question 7 months ago, created a question with more than 1,000 views. For Filtering SNPS by minimum LD value in bcftools?
Popular Question 11 months ago, created a question with more than 1,000 views. For rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
Scholar 11 months ago, created an answer that has been accepted. For C: Excel: using quartiles & averageifs to combine probe values without outliers
Popular Question 16 months ago, created a question with more than 1,000 views. For how do you remove the trace in heatmap.2 in R?
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