User: RNAseqer
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
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C: Is miarma-Seq being maintained?
... Thank you! I missed that bit. ...
written 7 weeks ago by
RNAseqer • 140
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... I was wondering if anyone uses miARma-Seq, and is it being maintained/kept up to date?
Thanks!
https://sourceforge.net/projects/miarma/
...
written 7 weeks ago by
RNAseqer • 140
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... 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 ...
written 10 weeks ago by
RNAseqer • 140
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... 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 ...
written 5 months ago by
RNAseqer • 140
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... 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 ...
written 7 months ago by
RNAseqer • 140
• updated
7 months ago by
Kevin Blighe ♦ 69k
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... 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 ...
written 8 months ago by
RNAseqer • 140
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... 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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... 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: ...
written 9 months ago by
RNAseqer • 140
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... 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! ...
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... 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 ...
written 9 months ago by
RNAseqer • 140
• updated
9 months ago by
Kevin Blighe ♦ 69k
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For No significant DEG: A request to double check my commands for limma.
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For No significant DEG: A request to double check my commands for limma.
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For Error "Bioconductor - mirna40cdf not available"
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For pulling snps from vcf file using ids
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For Filtering SNPS by minimum LD value in bcftools?
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For How to in R: Include principal components as covariates in analysis
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For Filtering SNPS by minimum LD value in bcftools?
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For rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
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For rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
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For C: Excel: using quartiles & averageifs to combine probe values without outliers
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