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yoshi's Content

There have been 4 items by yoshi (Search limited from 19-April 20)

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#172486 Chi-Square Vs Student's T Test

Posted by yoshi on 11 January 2015 - 11:04 PM in Bioinformatics and Biostatistics

If you pool the replicates you will get the same significance results for a 2x2 chi-square as for a t-test of the proportions.


A Mantel-Haenszel Test will make sure the replicates of a chi-square are not significantly different (there are other tests that do a similar thing).


Hi DRT, thanks. I've tried that before posting my problem here. And I just tried it again in case I have made a mistake previously. But even when I pool the samples (Treated: 78+ 482- and Non-treated: 403+ 2917-), and do a chi-square or Fisher's exact test, I got a p value of around 0.2. Have I missed something here?

#172477 Chi-Square Vs Student's T Test

Posted by yoshi on 11 January 2015 - 05:54 AM in Bioinformatics and Biostatistics

Hi All, my data looks like this:


Treated (4 replicates): (1) 21 positive, 178 negative (10.55% positive), (2) 25+, 166- (13.09% +), (3) 25+, 185- (11.9% +) and (4) 7+, 53- (11.67% +) 

Non-Treated (3 replicates):  (1) 131 positive, 1285 negative (9.25% positive), (2) 133+, 1264- (9.25% +), (3) 139+, 1368- (9.22% +)


I want to know if there's any significant difference between treated and non-treated.


I could either do a chi-square for each replicates against one of the non-treated, so that the 2x2 table would look like this:


Treatment:          21+     178-

Non-treatment: 131+     1285-



or I could do a student's t test, in which I first calculate the mean % positive for all 4 treated samples, and compare it against the mean % positive for all 3 non-treated samples.


The problem: Results are non-significant with chi-square but they are with student's t test. I am of course very tempted to use the latter test, but I would also like to confirm with experts here that it's correct for me to do so. I know that the 2 tests are investigating slightly different questions (chi-square: association between treatment and outcome and student's t test: difference between means). But from a biologist's point of view, the distinction is not that clear. Please advise.   

#164244 Weird fragments in my gDNA

Posted by yoshi on 16 January 2014 - 01:09 PM in Molecular Biology

Since there are consistently 2 bands of the same size at the low molecular weight region, I would guess that they are RNA rather than degraded DNA. Do keep in mind that RNA do not run like DNA on a non-denaturing gel.

#164095 Cre-Lox Recombination Technology

Posted by yoshi on 13 January 2014 - 09:38 AM in Molecular Biology

Dear All, I have a question about the Cre-Lox recombination technology. When a piece of DNA is flanked by a pair of inverted LoxP sites, the DNA will be inverted in the presence of Cre recombinase. I was just wondering, since the LoxP sites are retained after recombination (unlike when they are in the same orientation; one of the two is excised with the DNA), wouldn't this result in reversion of the DNA back to its original orientation if Cre recombinase is still present?


Also, I know that tissue culture-grade Cre recombinase is available commercially, but does anyone have any experience using it in suspension cultures?


Thanks in advance!

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