User: Avro

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Avro130
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Posts by Avro

<prev • 52 results • page 1 of 6 • next >
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Comment: C: I have two questions of spike-in data sets for microarray experiments
... 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 Avro130
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I have two questions of spike-in data sets for microarray experiments
... 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 ...
microarray written 3.7 years ago by Avro130 • updated 3.7 years ago by JC7.8k
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Comment: C: Simple question about deleted genes
... 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 Avro130
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Answer: A: Simple question about deleted genes
... 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 Avro130
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Comment: A: Simple question about deleted genes
... 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 Avro130
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Simple question about deleted genes
... 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! ...
acgh written 4.0 years ago by Avro130
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Why do focal aberrations in cancer more intense than arm-length aberrations?
... 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! ...
cancer written 4.0 years ago by Avro130 • updated 4.0 years ago by fongchunchan10
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Comment: C: I have to learn another language, but which one?
... 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 Avro130
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Forum: (Closed) I have to learn another language, but which one?
... 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 ...
forum programming written 4.2 years ago by Avro130 • updated 4.2 years ago by Michael Dondrup46k
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I am having trouble putting multiple maf alignments into one file so the parser can identify it as two alignments
... 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_ ...
maf written 4.2 years ago by Avro130

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For Where can I get the mouse mm9 gene annotation file?

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