Hi Yogi,
The detection rate is in the normal range and it depends on the
biological
samples. Actually, you should check the number of Presented probes,
instead
just the detection rate. For your case, it has more than ten thousand
probes
are Present, which is reasonably good. You can lower the p-value
threshold
to 0.05 to get more genes.
Pan
On 4/24/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at="" stat.math.ethz.ch=""> wrote:
> Message: 12
> Date: Thu, 24 Apr 2008 16:21:49 +1000
> From: "Yogi Sundaravadanam" <yogi.sundaravadanam at="" agrf.org.au="">
> Subject: [BioC] Detection slot - Lumi
> To: bioconductor <bioconductor at="" stat.math.ethz.ch="">
> Message-ID: <h000029400465e39.1209018106.mailmaster.agrf.org.au at="" mhs="">
> Content-Type: text/plain
>
> Hi All
>
> For 46628 features (illumina Mouse chip), one of my sample has
roughly
> about 22% of the genes that are detectable at a detection P value of
1%
> (according to the QC summary in lumi package).
>
>
>
> I am not sure if this is considered BAD? I tried reading about this
but
> don?t seem to get anywhere. Any pointers will be of great help
>
>
>
> Thanks heaps
>
> Yogi
>
Hi all,
I am trying to dowload a set of data samples from GEO database by
using
GEOquery package:
Example:
-------------------------------
library (GEOquery);
gds <- getGEO("GDS1047");
gpl<-getGEO("GPL198");
MA <- GDS2MA(gds, GPL = gpl);
--------------------------------
By the GEOquery user manual, this result in a MAlist containing all
details about the experiment.
As far as I understand, the MAlist object is used for storing M values
and A values, amongst other details.
* M values are defined as the logRatio of all genes in each
comparison.
* A values are defined as the average of logIntensities for each
comparison.
However, the MAlist created with GDS2MA seems not to store in "M" the
logRatios but only the intensities corresponding to every GSM in the
dataset.
I need to use the logRatios (M) of a lot of experiments and I would
write an script that automatically download and store these M values
in
tables.
Obviously, the script should be able to deduce which comparisons are
involved in the dataset (which GSM are numerators and which are
denominators)
Now I can store the intensities of the GSMs, but to convert these
intensities in ratios I need to check which are the comparisons by
hand... I would like to avoid this.
Any help?
Thanks in advance!
Best,
Juan Carlos
--
Juan Carlos Oliveros
BioinfoGP, CNB-CSIC
** NEW EMAIL ADDRESS: oliveros at cnb.csic.es **
On Thu, Apr 24, 2008 at 9:52 AM, Juan C Oliveros Collazos
<oliveros at="" cnb.csic.es=""> wrote:
> Hi all,
>
> I am trying to dowload a set of data samples from GEO database by
using
> GEOquery package:
>
> Example:
> -------------------------------
>
> library (GEOquery);
>
> gds <- getGEO("GDS1047");
>
> gpl<-getGEO("GPL198");
>
> MA <- GDS2MA(gds, GPL = gpl);
> --------------------------------
>
> By the GEOquery user manual, this result in a MAlist containing all
> details about the experiment.
>
> As far as I understand, the MAlist object is used for storing M
values
> and A values, amongst other details.
>
> * M values are defined as the logRatio of all genes in each
comparison.
>
> * A values are defined as the average of logIntensities for each
comparison.
>
> However, the MAlist created with GDS2MA seems not to store in "M"
the
> logRatios but only the intensities corresponding to every GSM in
the
> dataset.
>
>
> I need to use the logRatios (M) of a lot of experiments and I would
> write an script that automatically download and store these M
values in
> tables.
>
> Obviously, the script should be able to deduce which comparisons
are
> involved in the dataset (which GSM are numerators and which are
> denominators)
>
> Now I can store the intensities of the GSMs, but to convert these
> intensities in ratios I need to check which are the comparisons by
> hand... I would like to avoid this.
Hi, Juan. GDS1047 is a single-channel experiment. Therefore, there
are not ratios and GEOquery can't know how to make such ratios. As
for downloading and determing pairings for making ratios, you will, in
general need to do that by hand.
Hope that helps.
Sean
