User: zx12as3420

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zx12as34200
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Posts by zx12as3420

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Comment: C: TCGA FPKM-UQ method theory
... I have find the RSEM, TMM. What can I estimate which methods adjust batch better? It's the boxplots are similar. ...
written 3 months ago by zx12as34200
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Comment: C: TCGA FPKM-UQ method theory
... My opinion the same as you. I have use RMA, after FPKM or others. I think I must adjust sequence issue, then adjust batch effect within samples. Right? Thank you. ...
written 3 months ago by zx12as34200
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Comment: C: TCGA FPKM-UQ method theory
... I want to compare genes within different samples. I think RNA-SEQ have to use normalization, like microarray analysis. Having to adjust batch effect. I think FPKM, RPKM, TPM, FPKM_UQ method can't compare within samples. I am not sure why GDC not provide others analysis method. What is your recommend ...
written 3 months ago by zx12as34200
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Comment: C: TCGA FPKM-UQ method theory
... Thank you response. The reference is better for me. Which is your suggestion about normalization for RNA-SEQ? ...
written 3 months ago by zx12as34200
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Comment: C: TCGA FPKM-UQ method theory
... I know that many lecture show FPKM/RPKM are not good. I have a idea that the FPKM/RPKM are not like normalization for each sample. Right? ...
written 3 months ago by zx12as34200
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Comment: C: TCGA FPKM-UQ method theory
... But this just statistic define. why it is related with protein. ...
written 3 months ago by zx12as34200
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Comment: C: TCGA FPKM-UQ method theory
... Thank you response. My problem is biological concept of the formula. Why " the total protein-coding read count is replaced by the 75th percentile read count value for the sample."? ...
written 3 months ago by zx12as34200
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TCGA FPKM-UQ method theory
... Hello everyone. Recently, I want to study TCGA data. I can't know the FPKM_UQ calculation formula relate with its depiction from TCGA website. They say "The upper quartile FPKM (FPKM-UQ) is a modified FPKM calculation in which the total protein-coding read count is replaced by the 75th percentile ...
rna-seq written 3 months ago by zx12as34200 • updated 3 months ago by i.sudbery2.4k

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