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"Log of R/G normalized ratio"

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smith Click to EMail smithClick to check IP address of the poster Jul-26-02, 12:58 PM (PDT)
"Log of R/G normalized ratio"
Hi:

We're beginning to collect some serious data here and I'm just now beginning to look into the subject of clustering (which I don't know anything about really).

So, I was surprised to find some of our more interesting spots don't have an entry for log(base2) of R/G normalized ratio (mean), a field of the result table. The spots look fine, but when I look at the data further I find that these spots have one thing in common: Ch2 Background (Median)= 0. We're using ScanAnalyze at the moment.

I don't know why this should prevent the log ratio from being calculated. I'm not even certain this is really my problem.

Any help on this would be appreciated (as always). If this isn't the appropriate forum for this sort of question, just let me know.

Thanks again,
Smith

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RE: Log of R/G normalized ratio, sherlock, Jul-29-02, (1)
RE: Log of R/G normalized ratio, smith, Jul-29-02, (2)

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sherlock Click to EMail sherlockClick to check IP address of the poster Jul-29-02, 08:38 AM (PDT)
1. "RE: Log of R/G normalized ratio"
Hi Smith,

I think this is a bug , where spots with a median background of zero don't get normalized values created.

The following changes should be made in LoadExpt2DB.pl (in the cgi-bin/SMD/queue/ directory:

In getNormValue_DAT:

change:

if ($list>0 &&
$list>0 &&
$list>0 &&
$list>0){

to:

if ($list > 0 &&
$list >= 0 &&
$list > 0 &&
$list >= 0){

In getNormValue_GPR:

change:

if ($list>0 &&
$list>0 &&
$list>0 &&
$list>0){

to:

if ($list > 0 &&
$list >= 0 &&
$list > 0 &&
$list >= 0){

In UpdateResultTable_DAT:

change:

my $CH2BN_MEDIAN = $CH2B_MEDIAN / $normvalue if ($normvalue != 0 && $CH2B_MEDIAN);
my $CH2DN_MEAN = $CH2IN_MEAN - $CH2BN_MEDIAN if ($CH2IN_MEAN && $CH2BN_MEDIAN);

to:

my $CH2BN_MEDIAN = $CH2B_MEDIAN / $normvalue if ($normvalue != 0 && $CH2B_MEDIAN >= 0);
my $CH2DN_MEAN = $CH2IN_MEAN - $CH2BN_MEDIAN if ($CH2IN_MEAN && $CH2BN_MEDIAN >= 0);

In UpdateResultTable_GPR:

change:

my $CH2BN_MEDIAN = $CH2B_MEDIAN / $normvalue if ($normvalue != 0 && $CH2B_MEDIAN);
my $CH2DN_MEAN = $CH2IN_MEAN - $CH2BN_MEDIAN if ($CH2IN_MEAN && $CH2BN_MEDIAN);

to:

my $CH2BN_MEDIAN = $CH2B_MEDIAN / $normvalue if ($normvalue != 0 && $CH2B_MEDIAN >= 0);
my $CH2DN_MEAN = $CH2IN_MEAN - $CH2BN_MEDIAN if ($CH2IN_MEAN && $CH2BN_MEDIAN >=0);

You'll also need to update the data in the database, such that those spots with a median background of zero do get their values created. An easy way to do this is to simply renormalize all experiments (or at least those that have any spots with a median background of zero). The batch renormalization tool should hopefully help with this. Let me know if you have any questions,

Cheers,
Gavin

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smith Click to EMail smithClick to check IP address of the poster Jul-29-02, 02:07 PM (PDT)
2. "RE: Log of R/G normalized ratio"
Hello Gavin!

I made the changes you suggested and renormalized my data and now all is well! Thanks for the quick response.

Bye for now,
Smith

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