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Question: HTqPCR Release 2.10
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gravatar for Heidi Dvinge
6.3 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k wrote:
Hi Victoria, > Dear Heidi, > > Do you still maintain the Bioconductor HTqPCR Release 2.10? > HTqPCR is currently at version 1.11.2, so I assume you mean the version corresponding to R 2.10. It's not maintained as such, but it's still available at http://www.bioconductor.org/packages/2.10/bioc/html/HTqPCR.html and I can think of no reason as such why it wouldn't still work. > We are trying to use it to read in a file from Fluidigm's Dynamic Array > (48.48). > We are getting weird results. > Hm, can you be a bit more specific here? > For example, our genes assayed are 'test' or 'reference' in the Fluidigm > csv file. > Reading in the csv, all genes are labeled 'target', none labeled as test > or reference ? ? > How are you actually reading in the file? I.e., what's the exact readCtData command you provide? Are 'test' and 'reference' supposed to be the gene classes? It sounds like they're all labelled 'target' per default, because the information about which column to use isn't passed on to readCtData. If you look at the documentation for readCtData, you may notice that if the parameter format="BioMark" is used, then the columns being read in are: column.info=list(flag="Call", feature="Name.1", position="ID", Ct="Value") So, per default no column is being read that specifies the 'type' of gene, which I suspect is what you're after. This is intentionally left blank, since not all Fluidigm files contain a column with this information or the column name changes. You may try using readCtData with your own information specified, i.e. column.info=list(flag="Call", feature="Name.1", position="ID", Ct="Value", type='INSERT YOUR OWN VALUE HERE') If this doesn't work, then gimme a shout, preferably including the exact commands you tried. Best, \Heidi > Is there some manipulation that needs to be done to the Fluidigm output > csv file prior to reading it in? > Any insight is greatly appreciated, or point us in the right direction. > > THANK YOU. > ~V > > -- > Victoria Brown-Kennerly > Washington University GTAC/GPS > > > The materials in this email are private and may contain Protected Health > Information. If you are not the intended recipient, be advised that any > unauthorized use, disclosure, copying, distribution or the taking of any > action in reliance on the contents of this information is strictly > prohibited. If you have received this email in error, please immediately > notify the sender via telephone or return email. >
ADD COMMENTlink written 6.3 years ago by Heidi Dvinge2.0k
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