User: vinayjrao
vinayjrao • 110
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Posts by vinayjrao
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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
vinayjrao • 110
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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
vinayjrao • 110
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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
vinayjrao • 110
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... 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. ...
written 5 weeks ago by
vinayjrao • 110
• updated
5 weeks ago by
Kevin Blighe ♦ 37k
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... 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
vinayjrao • 110
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... 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
vinayjrao • 110
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... Hi, if you need the entire information for each of those, you could easily grep them out. ...
written 7 weeks ago by
vinayjrao • 110
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... 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
vinayjrao • 110
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... 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
vinayjrao • 110
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... 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 ...
written 8 weeks ago by
vinayjrao • 110
• updated
8 weeks ago by
Kevin Blighe ♦ 37k
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