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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... 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 10 weeks 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 4 months ago by
RNAseqer • 140
• updated
4 months ago by
Kevin Blighe ♦ 66k
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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 5 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 5 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 5 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 6 months ago by
RNAseqer • 140
• updated
6 months ago by
Kevin Blighe ♦ 66k
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... For the sake of completeness, in case anyone else digs up this post and finds it useful, here are some additional methods I wound up trying besides the use of quartiles shown above:
Taking the Standard deviation and dropping values more than 2* the Standard deviation from the mean (this method may ...
written 8 months ago by
RNAseqer • 140
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... Yes... I HAVE had run ins with that scoundrel Clippy before, and am well aware of the problems with excel. Taking your gentle hint I have gone and tried to solve the problem in R. Here is what I've come up with:
Adapting some R code from the links at the bottom I have done the following:
> ...
written 8 months ago by
RNAseqer • 140
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... Hello all, I am looking for an excel wizard to help me with a messy task: I would like to take the average of values in one column for all those cells sharing an ID in another column BUT with the added stipulation that outliers are excluded based on the use of quartiles.
Here is an example of the ...
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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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