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Forum: RNA Sequencing 07-12-2017, 01:59 AM
Replies: 4
Views: 3,850
Posted By granger
@peromhc Yes it is, but the problem with the...

@peromhc Yes it is, but the problem with the above tx2gene mapping is that it maps one transcript to multiple genes. Best is to keep track of gene ids removed.

A similar problem I came across:...
Forum: RNA Sequencing 12-01-2016, 10:21 AM
Replies: 4
Views: 3,850
Posted By granger
Smile Thanks sulicon, that helped. btw a quick way to...

Thanks sulicon, that helped.
btw a quick way to remove those rows in R:
tx2gene <- tx2gene[!duplicated(tx2gene$ens_id_version), ]
Forum: Bioinformatics 08-22-2016, 11:30 AM
Replies: 2
Views: 1,755
Posted By granger
Thanks. So either the single-cell protocol failed...

Thanks. So either the single-cell protocol failed to properly amplify the brain reference (denominator) and/or overamplified the human ref (nominator) compared to the original protocol....
Forum: Bioinformatics 08-16-2016, 09:56 AM
Replies: 2
Views: 1,755
Posted By granger
Unhappy Help interpreting this fold change plot

I came across this FC plot showing "agreement" between the Nanostring nCounter Single Cell Gene Expression method and the normal (multicell) one.
http://www.nanostring.com/products/single_cell
...
Forum: Bioinformatics 07-17-2016, 10:14 AM
Replies: 0
Views: 1,178
Posted By granger
Question Nanostring nCounter: determining presence of target?

The Nanostring Data analysis user manual describes options for determining presence or absence of target transcripts:

However, I am questioning the validity of the second approach: the data are...
Forum: Bioinformatics 07-17-2016, 09:48 AM
Replies: 0
Views: 4,146
Posted By granger
Exclamation Warning for Nanostring nSolver users

For those who work with nCounter rcc files from two or more similar codesets (rlf) and have no calibrator sample:
the program finds the common genes between codesets as it should, but then...
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