User: ab123

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ab12340
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London
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6 months ago
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2 years, 7 months ago
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Posts by ab123

<prev • 48 results • page 1 of 5 • next >
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Comment: C: rwehrens BatchCorrMetabolomics: doBC results in NA
... Finally solved this by taking a closer look at the raw code. Just in case someone has the same problem in the future: It was the minBsamp argument which requires a specified number of reference samples for each batch. If that number doesn't match or is not even across the dataset, the algorithm prod ...
written 6 months ago by ab12340
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Comment: C: GRCH38 counts significantly lower than for version 37?
... I am not entirely sure if version 38 really would only contain 17,000 genes? It refers to the final counts that are then used for diff. expr. analysis. Would version 38 contain significantly fewer genes? ...
written 6 months ago by ab12340
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GRCH38 counts significantly lower than for version 37?
... Hi there, Quick question: are the gene annotations specific to the sequencing platform for RNA-Seq? I'm looking at a dataset produced with Illumina HiSeq 2500. I've aligned it both with Human GRCH 38 and the older 37 version. So far so good...alignment files are the same sizes. When I then c ...
annotation grch rna-seq ensembl written 6 months ago by ab12340
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rwehrens BatchCorrMetabolomics: doBC results in NA
... Hi folks, Wondering if anyone could help: I've formatted my data to resemble the example data so I'm not getting what should be wrong here. Trying to use doBC but only getting a logical with NAs on return. I checked that all the inputs were the same as the example data and there doesn't seem ...
rwehrens batchcorrmetabolomics written 6 months ago by ab12340
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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 7 months 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 7 months ago by ab12340
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Comment: C: Univariate testing before or after feature selection
... Great answer! Thank you Kevin! ...
written 11 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 11 months ago by ab12340 • updated 11 months ago by Kevin Blighe44k
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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 12 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 12 months ago by ab12340

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