User: sumithra.das

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sumithra.das10
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Posts by sumithra.das

<prev • 13 results • page 1 of 2 • next >
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Comment: C: calculation of Z-score from Isoform expression data
... Thanks for your reply, b.nota. i think i better understand Z-score now. ...
written 2.5 years ago by sumithra.das10
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Comment: C: calculation of Z-score from Isoform expression data
... thanks for that, the data i'm working is within sample normalized, so for comparing a single isoform (X) expression across different samples i wanted to calculate Z-score. To do so, should i consider only the mean and standard deviation of X or mean and standard deviation of all isoforms( +73K isofo ...
written 2.5 years ago by sumithra.das10
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Comment: C: calculation of Z-score from Isoform expression data
... thank you, but for scaling and centering what should be my reference population?? ...
written 2.5 years ago by sumithra.das10
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Comment: C: calculation of Z-score from Isoform expression data
... sorry but how does scaling and centering help in Z-score calculation. plz explain. thanks ...
written 2.5 years ago by sumithra.das10
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calculation of Z-score from Isoform expression data
... Dear all, I'm using level 3 RSEM normalized data from GDAC Firehose, I want to compare the expression of an isoform across tumor samples of an cancer by calculating Z-score. so, my question is, to calculate Z-score of an Isoform (X), what should be the reference population & how to calculate ...
rna-seq written 2.5 years ago by sumithra.das10
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Comment: C: TCGA data: comparision in normal and tumor samples
... Hello, I'm using level 3 normalized data from GDAC Firehose, I have question reg. Z-score calculation in tumor sample alone. so, to calculate Z-score of a gene (X) in a tumor sample, how to calculate the mean & std.dev of reference population Z_Score = (expression in X in tumor ...
written 2.5 years ago by sumithra.das10
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Comment: C: RNA-Seq analysis for individual genes
... sorry but can you explain wat do you mean by bootstrapping in kallisto/salmon ...
written 3.0 years ago by sumithra.das10
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Comment: C: RNA-Seq analysis for individual genes
... Thank you for the link ...
written 3.0 years ago by sumithra.das10
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Comment: C: RNA-Seq analysis for individual genes
... thank you james, I am looking at transcript level expression, can i use directly the level 3 RSEM isoform values or is it good to take the raw counts and perform cufflinks and other packages as mentioned to understand expression and correlation. which would be a better input (RSEM/RPKM/TPM) for stu ...
written 3.1 years ago by sumithra.das10
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Comment: C: Which version of UCSC annotation are used in TCGA RNASeqV2 isoforms expression d
... Hi johanna, The link is not accessible now as TCGA portal is no longer operational, can u tell me an alternative link to know the version of UCSC annotation used in TCGA RNASeqV2 isoforms expression data? ...
written 3.1 years ago by sumithra.das10

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Popular Question 17 months ago, created a question with more than 1,000 views. For RNA-Seq analysis for individual genes

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