As always, excellent. I am but a simple clinician and your videos are helping me so much with my thesis. Can’t wait for the tutorial video; I am currently trying to do a pathway analysis correlating HPV gene expression in HPV positive HNSCC. Thank you!
Great video! I have used signed network and have about 20 modules. I correlated these modules to clinical traits. I have positive and negative module-trait correlations. But I’m not sure how to interpret the sign since we used an Eigengene. Would positive correlation with trait mean that genes in the module become more expressed as trait increases (eg. continuous trait type) ? And for negative, it means inverse relationship ?
Thank you very much for the excellent explanation. I am going to perform the WGCNA analysis as well. I have two questions hopefully you could provide some advice. 1. I only have 11 samples with 4 conditions, I really want to perform WGCNA analysis on the data. Does the performance decrease a lot? 2. The soft threshold given is 1. I don't know if this is due to the fewer sample numbers. I wonder if I could change the power to a higher value? Appreciate any suggestions.
HI, thank you for the very clear explanation. i have a request. Can you do for label free quantified proteomics data, where there are many missing values for genes between different variables
Thank you. Does the trait has to be continuous variable to relate the module with the trait. I have a data in which I categorize the brain region gene expression as prenatal and postnatal.
Not necessarily, discrete traits can also be associated with modules. I have spoken about this here - ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-mzXIxjPr_Mc.html
Thank you very much for the video! I will perform a RNAseq experiment and i'd like to know your opinion about the number of replicates and the sequencing depth. I was planning to sequence 5 replicates at 100M reads / samples (paired end). My goal is to discover driver genes for a particular pathway. With 5 replicates would it be possible to do this analysis with high accuracy, or is it better to do it with 10 replicates and half of the depth? My organism doesn't have its genome sequenced.
Hello mam, i am working on WGCNA in R and i am facing error in soft threshold power function. I am using gene_count.matrix txt file of RNA-seq, please help me to resolve the error . sft = powers = c(c(1:6), seq(from = 18, to=30, by=2)) pickSoftThreshold(datExpr0, powerVector = powers, verbose = 5) pickSoftThreshold: will use block size 1435. pickSoftThreshold: calculating connectivity for given powers... ..working on genes 1 through 1435 of 31169 Error in { : task 1 failed - "'x' has a zero dimension."
