[BioC] HTqPCR Release 2.10

[Heidi Dvinge]

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
>
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