User: Avro
Avro • 130
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Posts by Avro
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... Hi! Thank you for your answers! So, this is done so we can compare mRNA expression between different platforms/conditions. It's a all about normalization. I'm sorry, but I don't understand your last sentence about using different concentrations of the same sequence.
So, these spike-ins are only goo ...
written 3.7 years ago by
Avro • 130
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... Hi everyone,
I am reading a book called "Statistics and Data Analysis for Microarrays Using R and Bioconductor". More specifically, I am looking at the limitations of microarrays, and I don't understand this sentence:
"The variance of average chip intensity among spike-in data sets is much lower t ...
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... Thanks!
I am making a presentation about the thresholds that I am using. I could write it in terms of % increase or decrease, no? For example: "The minimal thresholds used were 0.1 (amplifications) and -0.1 (deletions). This translates to 1.07 (2^0.1) and 0.93 (2^-0.1). Essentially, an allele is c ...
written 4.0 years ago by
Avro • 130
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... Thanks!
I am making a presentation about the thresholds that I am using. I could write it in terms of % increase or decrease, no? For example: "The minimal thresholds used were 0.1 (amplifications) and -0.1 (deletions). This translates to 1.07 (2^0.1) and 0.93 (2^-0.1). Essentially, an allele is c ...
written 4.0 years ago by
Avro • 130
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... Hi Devon, Thank you for your quick response. I understand now! Basically, it is the cells with 0 copies that bring the ratio very low, right? Essentially, a cell can either have 0,1,or 2 copies. As for 1/2, then is it safe to suggest that cells are hemizygous (i.e. physical loss of one allele)? I do ...
written 4.0 years ago by
Avro • 130
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... Hi everyone,
I have a simple question about aCGH data: if you have two copies per gene and your log2 ratio is cancer/normal, how can you observe log2 = -4? That means 1/16... 16 original copies? I understand log2 = -1 (1/2).
Thank you!
...
written 4.0 years ago by
Avro • 130
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... Hi everyone,
I am using aCGH data. I have noticed that focal events are much more aberrated than arm-length (i.e higher log2 ratio). I am looking for a biological explanation. Does someone have an idea or could please refer me to some articles?
Thank you!
...
written 4.0 years ago by
Avro • 130
• updated
4.0 years ago by
fongchunchan • 10
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... Thanks! I think python is getting much better because of its scientific toolboxes. But to build standalone programs (which I won't really do), Java seems to be the best option.
...
written 4.2 years ago by
Avro • 130
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9 follow
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... Hi everyone,
I have learned how to program in R for bioinformatics. However, I am interested in learning another language seriously. I used java and C++ in the past, but python seems quite popular. Java is quite multifunctional (GUI,....). I would appreciate the community's feedback. Python seems t ...
written 4.2 years ago by
Avro • 130
• updated
4.2 years ago by
Michael Dondrup ♦ 46k
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... Hi everyone!
I have a large file of maf alignments for multiple non-coding RNA. I want to use the RNAz server (http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi) with the standard analysis. Here is an example of two maf alignments:
Alignment 1
##maf version=1
# maf_parse -s 1000 -e 1100 chromosome_1_ ...
written 4.2 years ago by
Avro • 130
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