User: ab123

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ab12340
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London
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Posts by ab123

<prev • 44 results • page 1 of 5 • next >
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Comment: C: Bash: salmon command not found
... Hi there, thanks for the answer. I followed the Salmon user script which doesn't mention the install command. I ran install and that seems to have solved the problem! Thank you! ...
written 6 days ago by ab12340
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Bash: salmon command not found
... Hello there, Has anyone gotten Salmon to work in Terminal? It keeps telling me that the command does not exist. I've already upgraded Anaconda and ran the command as just "activate salmon" instead of "conda activate salmon". The file has also been removed from the bash_profile as recommended i ...
salmon rna-seq bash written 6 days ago by ab12340
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Comment: C: Univariate testing before or after feature selection
... Great answer! Thank you Kevin! ...
written 4 months ago by ab12340
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Univariate testing before or after feature selection
... Hi there, Wondering if univariate have to be run before features are selected or can be applied to the selected features? The latter gives me better results. I understand that we select features to build the best predictive models, but in my case they also seem to bring out the most significant v ...
stats ttest written 4 months ago by ab12340 • updated 4 months ago by Kevin Blighe32k
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Analysing dose data separately or together
... Hi there, Just a quick question regarding analysis of dose-control data. I've got paired cell data with 5 biological replicates: 5x controls, 5x dose1, 5x dose2, 5x dose3, 5x dose4, and 5x dose5. I've selected the most important features using multivariate tools on the entire data set with all do ...
multivariate limma plsda written 4 months ago by ab12340
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Comment: C: Repeated Measures or Not
... Ah, thank you. So you're saying the doses themselves are independent. So if I apply dose 1ug/ml, 2, 3, 4, 5 to Biorep 1, then these are independent as well. ...
written 5 months ago by ab12340
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Comment: C: Repeated Measures or Not
... You forget that the flasks are plated in 10x 6-well plates, so you are spreading out the bio reps. Ignore the tech reps within these plates, they are not important here > they're merely for biomass. I.e. Biorep 1 is exposed to 5 doses across say 5 well plates. ...
written 5 months ago by ab12340
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Repeated Measures or Not
... Hello there, Quick conceptual question over whether this experiment truly would reflect a repeated measure or whether samples are indeed independent. I have a cell culture that is grown in 5 different flasks to produce 5 biological replicates. These are then split further into 10x 6-well plates ...
linear regression repeated measures limma written 5 months ago by ab12340
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Metafor microarray meta-analysis inputs
... Hi there, I'm trying to run meta-analysis of multiple data sets (microarray) using metafor. However, I'm struggling to understand the input. I've already preprocessed the data and have my differentially expressed genes from limma. The metafor function is: rma(yi, vi, sei, weights, ai, bi ...
metafor meta-analysis written 7 months ago by ab12340
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From metabolites to genes
... Hi there, Are there any recommended tools to determine the genes linked to certain differentially expressed metabolites? Any help much appreciated. Thank you. ...
metabolomics genomics written 10 months ago by ab12340 • updated 10 months ago by Kevin Blighe32k

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