Moderator: b.nota

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b.nota5.4k
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Posts by b.nota

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Comment: C: RNA Expression Pathway Database
... I am afraid that what you want: "expression of X causes an increase/decrease in the expression of Y" is too simplistic for real biology. What I mean is that biology is more complex than finding one to one gene expression relationships. Databases containing data with "protein X binds protein Y" or " ...
written 2 days ago by b.nota5.4k
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Comment: C: FASTQ alignment result is really bad
... Can you show with head how your fastq file looks like? Is it really in color space? ...
written 3 days ago by b.nota5.4k
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Comment: C: FASTQ alignment result is really bad
... Please read more about Solid data conversion to fastq [here][1]. You probably lose information with the conversion to fastq. [1]: https://www.biostars.org/p/45631/ ...
written 3 days ago by b.nota5.4k
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Comment: C: Terrible RNA mapping result by STAR
... Too short means too short alignment. Are you sure you use the right reference? ...
written 3 days ago by b.nota5.4k
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Comment: C: how to plot PCA for microarray normalized data
... Let's show an example with random data, because I don't have your RMA values. # Let's make a random matrix first set.seed(11) emptyMatrix <- matrix(nrow = 19000, ncol = 18) randomMatrix <-apply(emptyMatrix, c(1,2), function(x) sample(c(1:16), 1)) colnames(randomMatrix) &l ...
written 3 days ago by b.nota5.4k
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Comment: C: how to plot PCA for microarray normalized data
... Did you look in the link I sent? I don't see anything about CDF file being necessary. > exprsFile <- file.path(dataDirectory, "exprsData.txt") > exprs <- as.matrix(read.table(exprsFile, header=TRUE, sep="\t", + row.names=1, + ...
written 3 days ago by b.nota5.4k
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Answer: A: how to plot PCA for microarray normalized data
... You can import normalized values into `limma`, using `ExpressionSet()` https://www.bioconductor.org/packages/3.7/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf. A PCA can be made in R with the `prcomp()` function https://stat.ethz.ch/R-manual/R-devel/library/stats/html/prcomp.html. ...
written 3 days ago by b.nota5.4k
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Comment: C: Getting unusual characters while generating output files in a bash script
... The unique read group header (`string` after `-R`) makes it a bit difficult for a `for` loop, unless you can extract that `string` easily? ...
written 4 days ago by b.nota5.4k
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Comment: C: EdgeR with Paired Sample Replicates
... Yes you are testing "exp" vs "ctrl" with this design, but with the "day" effect taken into account (think of it as a similar approach to a paired t-test). ...
written 4 days ago by b.nota5.4k
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Answer: A: EdgeR with Paired Sample Replicates
... If you want to include `"paired"` in your design, you should not make the `group` factor, but include both `experiment` and `day` in the design. experiment <- factor(targets$Experiment) day <- factor(targets$Day) design <- model.matrix(~0+experiment+day) # Depending on ...
written 4 days ago by b.nota5.4k

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Scholar 15 days ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Popular Question 7 weeks ago, created a question with more than 1,000 views. For phred 33 from Ion S5?
Scholar 10 weeks ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Popular Question 12 weeks ago, created a question with more than 1,000 views. For RNAseq analysis with Ion AmpliSeq Transcriptome Solution data
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Scholar 4 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Popular Question 4 months ago, created a question with more than 1,000 views. For RNAseq analysis with Ion AmpliSeq Transcriptome Solution data

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