User: grayapply2009
grayapply2009 • 170
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Posts by grayapply2009
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... That sounds reasonable, goodez. ...
written 17 months ago by
grayapply2009 • 170
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... But the ratio should not change, right?
RNAseq: Variant 1 / Variant 2 = 25
qPCR: Variant 1 / Variant 2 = 10
How do you explain this? ...
written 17 months ago by
grayapply2009 • 170
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... Another question, we did qPCR to validate the RNAseq results. We found less difference between our "major isoform" and all other isoforms than what we found in RNAseq. Is this just a technical difference or does this have something to do with biology? ...
written 17 months ago by
grayapply2009 • 170
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6 follow
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... We recently did RNA-seq for our samples and quantified the expression levels of the 7 transcripts of one gene. We found one of these transcripts are expressed significantly higher (30x) than other transcripts across all of our samples.
Any explanation for this constantly high expression for a singl ...
written 17 months ago by
grayapply2009 • 170
• updated
12 months ago by
kristoffer.vittingseerup • 2.6k
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Comment:
C: Sample size too small for ARACNE
... Thank you very much for replying my post. There is a computer algorithm (ARACNE) that can reconstruct gene regulatory networks from gene expression profiles. However, it requires a minimum of 100 gene expression profiles, for example, 100 microarray datasets. I only have 20 of these datasets so I gu ...
written 2.7 years ago by
grayapply2009 • 170
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... Thank you, gaoce. That works perfectly. Where can I get the tutorial for this? The GEOquery document doesn't seem to have what you guys showed me above. ...
written 3.2 years ago by
grayapply2009 • 170
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... Thank you Sean. Now how can I export the Series Matrix file with the probes replaced by gene symbols? ...
written 3.2 years ago by
grayapply2009 • 170
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... Hi,
I read the GSE file into R as follows.
gse <- getGEO("GSE4928", GSEMatrix=TRUE)
Now I want to convert all probe IDs to gene symbols and write the entire annotated dataset back to my computer. What should I do?
By the way, which dataset is stored in gse? SOFT formatted family file, MINiML ...
written 3.2 years ago by
grayapply2009 • 170
• updated
3.2 years ago by
Sean Davis ♦ 25k
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... I have a microarray data set. The format is like this:
a 12 13 14
b 15 16 17
a 21 22 23
b 24 25 26
Now I want to collapse and average all rows and columns based on the gene name (the 1st line). The desired results:
a 16.5 17.5 18.5
b 19.5 20.5 21.5
T ...
written 3.2 years ago by
grayapply2009 • 170
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Comment:
C: Pooling microarray data
... Looks like a lot of trouble. I'll just merge the arrays done on the same platform I can find. Thank you very much, Jean. ...
written 3.2 years ago by
grayapply2009 • 170
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