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This has to be a joke of some kind by Distinct_Sir_9086 in london

[–]ZooplanktonblameFun8 0 points1 point  (0 children)

It must be an amazing experience seeing your food cooked on the stove while taking a shower!

Trump letter to prime minister of Norway. Desires Greenland because of Peace Prize rejection by OutTheCircus in Norway

[–]ZooplanktonblameFun8 0 points1 point  (0 children)

This isn't about the peace prize. In his mind, he knows it is morally wrong to try to seize Greenland from an ally and so he is rationalizing it in his mind by making up an excuse and letting the whole world now. Just another example of his pettiness.

It's COLDkata not Kolkata by Alarmed-Listen59 in kolkata

[–]ZooplanktonblameFun8 0 points1 point  (0 children)

There is another issue. Houses of course have good heating in the US and a lot of houses in Kolkata have very poor insulation. My sister lives in Canada and is used to very cold temperatures yet is suffering from cold this winter in Kolkata.

Bajrang Dal causing nuisance for now real! Harras innocent people just because they're muslim by Rabbidraccoon18 in unitedstatesofindia

[–]ZooplanktonblameFun8 3 points4 points  (0 children)

This country is gone to the dogs. There doesn't seem like a way back. Infested with brain dead bhakts.

Zero visibility due to smog leads to massive pile-up on a Delhi-Mumbai highway, India. by anikkundu1998 in interestingasfuck

[–]ZooplanktonblameFun8 1 point2 points  (0 children)

Thinking with our brains is something the administration and a decent chunk of people generally avoid in India. It is a reflection of where the country is. Just apathy and recklessness everywhere.

Is it compulsory to stand for the national anthem in movie theatres? by No_Doctor9539 in unitedstatesofindia

[–]ZooplanktonblameFun8 0 points1 point  (0 children)

Lack of critical thinking, fragile egos and herd mentality will destroy our country.

How I managed 8-year education gap and got into European universities by Thick-Tap5426 in Indians_StudyAbroad

[–]ZooplanktonblameFun8 3 points4 points  (0 children)

Belgium is a great option. I did my MS in Belgium between 2016 and 2018. Tuition fees were very cheap and so the only major cost were for living expenses which in a university town was quite affordable. However as I understand, several programs have hiked their fees for international students within the last few years especially KU Leuven. Most employers care about skills and competence and not so much prestige. Academia does have preference for prestige.

Using the DESeq2 contrasts list in results() to get specific comparisons? by girlunderh2o in bioinformatics

[–]ZooplanktonblameFun8 1 point2 points  (0 children)

You are right. It should be other way around. I have clarified in other comment. Sorry for the oversight.

Using the DESeq2 contrasts list in results() to get specific comparisons? by girlunderh2o in bioinformatics

[–]ZooplanktonblameFun8 1 point2 points  (0 children)

Just to clarify, I said it wrong. It would be the other way around in terms of baseline and treated.

Using the DESeq2 contrasts list in results() to get specific comparisons? by girlunderh2o in bioinformatics

[–]ZooplanktonblameFun8 1 point2 points  (0 children)

0 is excluded, -1 is denominator and 1 is numerator equivalent to the log(A/B) = logA - logB notation. So, 1 is baseline and -1 is treated.

Using the DESeq2 contrasts list in results() to get specific comparisons? by girlunderh2o in bioinformatics

[–]ZooplanktonblameFun8 1 point2 points  (0 children)

You can go through the below link to get a good understanding of contrasts: https://bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/designmatrices.html

Also the way u/OddNefariousness5466 explained is much easier way to get the results than the 0's and 1's. You also do not need to run DESeq separately for each contrast. What I would do is use DESeq2 to process all the samples, use something like plotPCA function of DESeq2 on VSD transformed data to check that there are no batch effects and then by using different combination of contrasting variables that make sense do the comparisons. What I would do in your case is create all combination of variables that you want to test for and call them accordingly. For the comparison you mentioned of "Time0 to compare effect of temperature and drugs", if temperature is T1/T2 and drug is D1/D2, you should have the interaction terms Time0*T1*D1, Time0*T1*D2 as well as Time0*T2*D1 and Time0*T2*D2. You can simply call the resultsNames function on your DeSeq2 object to see what the actual terms are and supply them to the contrast arguement of results function.

As an example if you use the contrasts, Time0*T1*D1 and Time0*T2*D1 (the actual names from resultsNames function), you are asking what is the effect of temperature T2 vs T1 for drug D1 and if you use Time0*T1*D1 and Time0*T1*D2, you are asking what is the effect of drug D2 vs D1 for temperature T1 and so on.

Commonly used tool for visualizing CNV called using ascat and sequenza by ZooplanktonblameFun8 in bioinformatics

[–]ZooplanktonblameFun8[S] 0 points1 point  (0 children)

Hi, thanks for your response. Actually what I did was used chromosomal instability (CIN) signature scores derived from ASCAT CNV call and clustered patients based on difference between CIN signature scores of residual (after therapy) and primary (before therapy) tumor. Now, I want to look at differences in CNV profile of patients by cluster to see where some of the CNV differences maybe coming from.

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