User: vinayjrao
vinayjrao • 120
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Posts by vinayjrao
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... Thanks Kevin, for the clarification. Although, I would like to know why I should remove these after normalization, and what is the significance of these positive control probes? ...
written 4 days ago by
vinayjrao • 120
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... Dear Kevin,
Thank you for your response. I am arranging some of the details below -
> ProbeUID ProbeName Sequence
> 51568 GT_Mm_44k_51_P314501 ACGTCGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCA
> 1164 (+)E1A_r60_1 `Sequence Column is Empty`
And you sai ...
written 5 days ago by
vinayjrao • 120
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... I want to be able to see the contents of each file imported using `readTargets`. Is that possible? ...
written 5 days ago by
vinayjrao • 120
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... Hi,
I am analyzing raw microarray data obtained using the Agilent system. When I was looking at the pre-analyzed results of the same data, I found that the two control samples were additive inverses of each other (-0.42, 0.42), thereby canceling each other to give a median log2FC of 0, but this tre ...
written 5 days ago by
vinayjrao • 120
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... Hi,
I am analyzing raw microarray data obtained using the Agilent system. While looking at the results table, I found that a lot of the probes do not have a probe sequence. Could someone please guide me through these probes? Are these used only by the system, and do not mean anything biologically?
...
written 5 days ago by
vinayjrao • 120
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... Dear Davy,
I understand that it has been a long time since your suggestion, but in my opinion, option 8 might be considered as cherry picking from the data, since you are only interested in ones with the lowest p-value, and that might not implicate the biological scenario, especially when we look i ...
written 5 days ago by
vinayjrao • 120
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... Hi Leite,
When I read the `targets.txt` file, will the individual files be accessible through R?
Thanks ...
written 6 days ago by
vinayjrao • 120
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... Hi,
To address a particular question, concerning a particular gene, which we hypothesize is involved in reducing DNA damage repair, we decided to analyze RNA-Seq data from TCGA. Upon analysis, we found that the particular gene is overexpressed in breast cancer, but we could not get an enrichment in ...
written 3 months ago by
vinayjrao • 120
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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 months ago by
vinayjrao • 120
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Comment:
C: Plotting TCGA's HM450 data
... Thanks a lot, Kevin. You have been extremely helpful. ...
written 5 months ago by
vinayjrao • 120
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