User: vinayjrao

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vinayjrao110
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Posts by vinayjrao

<prev • 116 results • page 1 of 12 • next >
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Comment: C: Plotting TCGA's HM450 data
... I have just another question. Is it acceptable to correlate expression and methylation pattern by plotting a PCC? If yes, should it be done by adjusting the RSEM counts from 0 to 1, or should it be done with the raw values? ...
written 5 weeks ago by vinayjrao110
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Comment: C: Plotting TCGA's HM450 data
... Thanks a lot, Kevin. You have been extremely helpful. ...
written 5 weeks ago by vinayjrao110
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Comment: C: Plotting TCGA's HM450 data
... Thanks a lot, Kevin. Can I directly correlate the methylation status with expression levels? For the same, gene, I am looking at the expression level and methylation status. So, if the RSEM value is for example, around 13000 (median), in breast carcinoma, and 20000 for glioblastoma. Corresponding m ...
written 5 weeks ago by vinayjrao110
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Plotting TCGA's HM450 data
... Hello, I want to look at the methylation pattern of the promoter around a certain gene in different cancers; TCGA data is obtained from cBioPortal. I want to know if the data (beta values) can be plotted directly, or do I have to normalize it by any way first. Thanks in advance. ...
hm450 tcga methylation bisulfite-seq written 5 weeks ago by vinayjrao110 • updated 5 weeks ago by Kevin Blighe37k
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Comment: C: Interpretation of Beta values : Methylation data
... Dear Devon, In this case (1), is it OK to consider that a value of 0.1 would indicate that 10% of my samples were methylated, while the rest were not? Thanks in advance ...
written 6 weeks ago by vinayjrao110
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Comment: C: Normalizing RPPA data counts from TCGA
... Hi, I'm sorry for the delay. After download the RSEM values, I merged them in order of the tumor type using shell. Without any further normalization, this data was imported to R and plotted. ...
written 7 weeks ago by vinayjrao110
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Comment: C: Can gffread extract specific region sequences from vcf or fasta file?
... Hi, if you need the entire information for each of those, you could easily grep them out. ...
written 7 weeks ago by vinayjrao110
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Comment: C: Normalizing RPPA data counts from TCGA
... Yeah, so we wanted to analyze RAN and protein expression for a couple genes. The RNA expression data were RSEM values. I also read that RSEM values are already normalized, so the question is to plot the absolute values of the log. ...
written 8 weeks ago by vinayjrao110
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Comment: C: Normalizing RPPA data counts from TCGA
... Hi Kevin, Thanks for the reply. If I don't consider the expression values with Z-scores, is it still acceptable? Also, I downloaded RSEM values (gene expression). Is it OK to plot the data as the absolute RSEM values, or log2(RSEM)? Thanks again. ...
written 8 weeks ago by vinayjrao110
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Normalizing RPPA data counts from TCGA
... Hello all, For a study, we decided to look into the expression levels of a particular gene in TCGA data, following which we were intrigued to look into the protein expression levels (RPPA) as well. The aforementioned data are all available on [cBioPortal][1]. My question is, what is method followe ...
tcga rppa protein expression written 8 weeks ago by vinayjrao110 • updated 8 weeks ago by Kevin Blighe37k

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