[BioC] Fold change GEO data

[Sean Davis]

On Sat, Sep 13, 2008 at 12:08 PM, hemant ritturaj
<ritturajhemant at gmail.com> wrote:
> Dear All,
>
>
> My question is when i used the GSE data
>
> gse <- getGEO('GSE7530')[[1]]
> exprs(gse) <- log2(exprs(gse)+1)
> Warning message:
> In log(c(-2.50293388, -2.043776569, 0.552862779, 0.551170135, -2.433251302,
> :
>  NaNs produced
>
> Quesion 1: I am not able to understand this error, is this mean that some of
> the point is not present in data, if yes how to tackle such problem ???

Note that this is not an error, but a warning.  As for why, if you
look at the raw data, you will see that it contains zeros.  You can
either add a small positive value to the expression values before
taking the log (see the previous email that I sent to you) or you can
use an approach like a glog (the bioc mailing list archive has a
discussion of glog from Wolfgang Huber).

> Keeping this problem in view  would it be fine to go further with the
> further steps ??

If your algorithms will deal with NaNs in the data, then you can
probably go ahead.

> I tried to save this expression information using
>> write.table(exprs(gse),file="gse_7530_exprssn",sep="\t")
>
> this file do have expression information but it doesn't have any probe name
> but jst the serial number of the probes, How can it be joined to the probe
> names.

You will need to write out the featureData as well.  See the
ExpressionSet help and Biobase vignettes for more information.

Sean