User: RNAseqer

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RNAseqer 130
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Very new to RNAseq, previous experience in genome assembly, phylogenetic analysis, substitution rate analysis etc etc.

Posts by RNAseqer

<prev • 84 results • page 1 of 9 • next >
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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 1 day ago by RNAseqer 130 • updated 1 day ago by Kevin Blighe60k
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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 5 weeks ago by RNAseqer 130
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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 5 weeks ago by RNAseqer 130
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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 6 weeks ago by RNAseqer 130
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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 weeks ago by RNAseqer 130 • updated 9 weeks ago by Kevin Blighe60k
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Comment: C: Excel: using quartiles & averageifs to combine probe values without outliers
... 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 3 months ago by RNAseqer 130
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Answer: C: Excel: using quartiles & averageifs to combine probe values without outliers
... 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 3 months ago by RNAseqer 130
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Excel: using quartiles & averageifs to combine probe values without outliers
... 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 ...
outliers quartile matching excel averageifs written 3 months ago by RNAseqer 130 • updated 3 months ago by swbarnes27.8k
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Comment: C: A good place to get immune cell deconvolution reference datasets?
... Thank you Kevin! I'm currently looking at Cellmix as a sort of 'first pass', but if the Abbas dataset is a typical or oft used reference I'll probably try to employ it whatever software I wind up using. Cellmix does seem to be a bit finicky... This is a microarray dataset I'm looking to wrap up wor ...
written 4 months ago by RNAseqer 130

Latest awards to RNAseqer

Scholar 3 months ago, created an answer that has been accepted. For C: Excel: using quartiles & averageifs to combine probe values without outliers
Popular Question 9 months ago, created a question with more than 1,000 views. For how do you remove the trace in heatmap.2 in R?
Rising Star 13 months ago, created 50 posts within first three months of joining.
Supporter 13 months ago, voted at least 25 times.
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