u/frustrated_870

Dear everybody,

I am a Bachelors student currently doing a placement in Cambridge University. I study in mainland Europe, where, to do a PhD, you have to do a Masters placement. I found out that in the UK you don't actually need a Masters to do a PhD, just a bachelors. I was thinking of doing a Masters anyway (and then a PhD), and although this peaked my interest I didn't think too much about it.

Anyway, talking to a PI recently at Cambridge, I apparently impressed and he is now interested in taking me on as a PhD after my Bachelors (I didn't ask for it he just offered).

I wanted to ask, what are the positives and the negatives of doing a masters first. Should I accept or say I would like to come back after two years. I have actually a fair bit of research experience already, from summer programs, the Amgen Research Program and internships during my studies.

I like the field of research he works in and have done some myself, but of course this is all coming at me very quickly.

Any advice would be much appreciated, especially fro those with PhD and academia experience in general.

Dear everybody,

I am a Bachelors student currently doing a placement in Cambridge University. I study in mainland Europe, where, to do a PhD, you have to do a Masters placement. I found out that in the UK you don't actually need a Masters to do a PhD, just a bachelors. I was thinking of doing a Masters anyway (and then a PhD), and although this peaked my interest I didn't think too much about it.

Anyway, talking to a PI recently at Cambridge, I apparently impressed and he is now interested in taking me on as a PhD after my Bachelors (I didn't ask for it he just offered).

I wanted to ask, what are the positives and the negatives of doing a masters first. Should I accept or say I would like to come back after two years. I have actually a fair bit of research experience already, from summer programs, the Amgen Research Program and internships during my studies.

I like the field of research he works in and have done some myself, but of course this is all coming at me very quickly.

Any advice would be much appreciated, especially fro those with PhD and academia experience in general.

Hi everyone! I have been doing cell cell communication analysis recently (using cell chat specifically), and I had a thought that is bugging me. Please bear with me as I am not an expert in cell cell communication or bioinformatics as a whole. Specifically, I am doing comparative cell cell communication analysis

If one dataset has more cells in general or of a specific kind than the other dataset, could this skew the analysis by assuming there is just more signals in general from a cell type without accounting that in fact there are more cells from that type? Cell number variations could occur easily from sampling, especially with low sample number. I'm working with spatial scRNA-seq, so the danger is even more so as it's a specific cut of a sample.

Could this initial skewness affect everything else downstream in CCC analysis?

I'm super sorry if it's a dumb question.

Cheers!

Hello everyone!

I've been working at a lab under a summer programme for the past couple of weeks and I am suffering slightly. My supervisor has given me some raw scRNA seq data, taking from an in situ imaging-based platform that targets about 1000 genes, and has sort of left me to my own devices with it (apparently he isn't very savvy with bioinformatics himself). Anyway, I am somewhat comfortable working in R and Python, and I am getting the hang of Seurat, so it hasn't been catastrophic.

However, I am now struggling with clustering my cells. The cell clusters that I am being given are not physiological, and tend to be large, varied groups, which makes it hard to define anything really. I know studies that have done similar things on similar tissues to mine (albeit with another method) and are getting far nicer clusters. In their methods they just say "oh, we followed the standard Suerat workflow, and badabim-badboom these are the results".

My UMAP seems to agree with the confusion in my clusters as it just seems like a smear, with different sides of the smear coloured different things by the clustering.

I have tried changing the clustering method (Leiden, igraph), the resolution, dimensions (although I try to keep it in line with my elbow plot). I have tried changing the normalisation and other preprocessing parameters, varying in. their forms and flavours. I even tried the newer SCT transform, which made a nicer UMAP but just as crap clusters.

I am feeling quite inept currently, and rather disheartened having lost a week and a bit at this (I don’t know if it's normal or not). I don't really have any one in my lab to reach out to either.

My question is, does anyone have any ideas what I could attempt next or what might be wrong? Any resources I could have a look at? Anything anyone could recommend would be amazing.

Sorry for the long post and thank you to all who may answer in advance.