User: krushnach80

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krushnach80200
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Posts by krushnach80

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Comment: C: performing a PCA on a gene set in R
... This is the order how columns are arranged where HSC is [H1-H4} , Monocyte is [M2-M4] , CMP is [C2-C4] ,GMP is [G2-G4], and Granulocyte is [Gran1- Gran2] Rest I have `AML samples like LSC,Blast, each 8 sample each .` So `HSC is [H1-H4} , Monocyte is [M2-M4] , CMP is [C2-C4] ,GMP is [G2-G4], an ...
written 1 day ago by krushnach80200
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Comment: C: performing a PCA on a gene set in R
... Im trying to make this `condition` data frame these are my sample names "H1" "H2" "H3" "H4" "M2" "M3" "M4" "C1" "C2" "C3" "C4" "G2" "G3" "G4" "Gran1" "Gran2" This is the order how columns are arranged where `HSC is [H1-H4} , Monocyte ...
written 1 day ago by krushnach80200
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Comment: C: Extracting features or gene from PCA after calculating PCA for downstream analys
... okay I was wondering that, as always your suggestion and codes are really helpful ...
written 2 days ago by krushnach80200
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Comment: C: Extracting features or gene from PCA after calculating PCA for downstream analys
... data.frame(sort(abs(project.pca$rotation[,"PC4"]), decreasing=TRUE)[1:50]) why you have mentioned "PC4"? isn;t that supposed to be PC 1 i was just wondering ...
written 2 days ago by krushnach80200
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Comment: C: Extracting features or gene from PCA after calculating PCA for downstream analys
... Yes in paper they tell they did but won't write about the exact method so how to order those eigenvalues ? ...
written 2 days ago by krushnach80200
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Comment: C: Extracting features or gene from PCA after calculating PCA for downstream analys
... okay...there is no definite method to do so...I was wondering how did they arrive at 500 genes in that paper ...Then will try ...do you have any tutorial for that or answered similar question how to take out genes contributing to PCA , if you had answered in the past it would be of great help to loo ...
written 2 days ago by krushnach80200
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Comment: C: Adding Percentage in PCA
... yes it is ....as such pca$rotation PC1 PC2 PC3 PC4 5S_rRNA -1.090574e-02 -2.412665e-03 1.637689e-02 -3.603865e-02 AB019441.29 -1.928250e-02 1.821083e-03 -9.713724e-03 -1.978 ...
written 2 days ago by krushnach80200
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Comment: C: Adding Percentage in PCA
... and how do i extract that? or get the gene from those principal component? is it just manual or method or can i do it a R ...
written 2 days ago by krushnach80200
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Extracting features or gene from PCA after calculating PCA for downstream analysis
... [Paper link][1] Im quoting their lines which is as such " We performed principal component analysis (PCA) of low-coverage sequencing data to identify genes explaining variation across cells. PCA separated the cells into groups corresponding to the source populations (Fig. 2c and Supplementary Fig ...
R written 3 days ago by krushnach80200 • updated 3 days ago by swbarnes22.9k
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Comment: C: Adding Percentage in PCA
... @Kevin I tried your code and checked project.pca$rotation it contains all the gene i use as i see the dimension of my input gene and project.pca$rotation are same except the non-numeric column , but is that in order?I mean the same as my input list ? ...
written 3 days ago by krushnach80200

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