User: Grace_G

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Grace_G0
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Posts by Grace_G

<prev • 22 results • page 1 of 3 • next >
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Comment: C: to get each covariate with PC loading in PCA
... hi, Ryan! Maybe the following related, however, it is really a good doc, so I share here. > Principal Variance Component Analysis (PVCA) to explore how technical > and biological factors correlate with the major components of variance > in the data set > > 3.6 F. Principal Variance C ...
written 2 days ago by Grace_G0
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Comment: C: to get each covariate with PC loading in PCA
... Seems very possible, many thanks for your time Ryan!!! ...
written 4 days ago by Grace_G0
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Comment: C: to get each covariate with PC loading in PCA
... Thanks! I guess it's colnames(sample id) are honey, winey, body,...and my are liver_female_2 heart_male_6 lung_female_3 liver_female_1..., organ's loading(liver, heart, lung), gender's loading(female, male), age's loading(2,6,3,1). The requirement for me is to get correlate every covariate (e.g. age ...
written 5 days ago by Grace_G0
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Comment: C: to get each covariate with PC loading in PCA
... Sorry, I afraid I can't, actually it's general. ...
written 5 days ago by Grace_G0
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Comment: C: to get each covariate with PC loading in PCA
... Yes, it like sometimes we hope wild type samples together and mutant type sample together on the PCA plot. Here I hope same organ sample together on PCA plot, this is what I mean "correction of samples". But after draw this plot, we want to know each covariate(organ, gender, age) with PC loading nex ...
written 5 days ago by Grace_G0
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Comment: C: to get each covariate with PC loading in PCA
... Thanks Ryan, glad to hear from you! I'm not sure, also not sure what as the input data, actually just want to see like pc1 or pc2 or pc10 loading age (and other covariates) most. But seem's rare PCA material about this, I'm seeking some package to do since now I also not sure the format of input dat ...
written 5 days ago by Grace_G0
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Comment: C: to get each covariate with PC loading in PCA
... Thanks, but not have covariate with PC loading part. ...
written 5 days ago by Grace_G0
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Comment: C: to get each covariate with PC loading in PCA
... Thanks for your view! But a file phenotype data is used for DEseq2, isn't it? Here for PCA not use DEseq2, since all these phenotype data are used for describing samples, so I combine them as sample ID directly, so sample ID can show all of them. read counts matrix like: liver_female ...
written 5 days ago by Grace_G0
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to get each covariate with PC loading in PCA
... Hello, I got the read counts matrix of sample after RNA-Seq htseq-count, for this read counts matrix, rownames are gene id, colnames are sample id(format, organ_gender_age),then use PCA to find correction of samples, but how to each covariate(organ, gender, age) with PC loading??? Any recommend w ...
pca rna-seq written 6 days ago by Grace_G0
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Comment: C: How to treat the pair-end files as single-end when RNA-Seq align?
... Thanks for your consideration, it's much helpful too. So for this star step, how about directly process these m samples as pair-end, n samples as single-end, since when they go to bam step, they will become same for next process? ...
written 10 weeks ago by Grace_G0

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