Lorena Pantano

Hi, Thank you for the questions. 1-that seems correct. But cluster ID is really Locus ID. 2-The sequences that are removed are the ones that map to many time to...

On October 17, 2019 at 12:18:28 AM, BioinfoHub-PeiQinNg ( [email protected]) wrote: Hi, Thank you for answering my questions. Just to clarify for 2- If I understood correctly, a locus that...

Hi @etbuface, thank you for the details. This function works in the following way: 1-make pair-wise correlations between the input genes (that they should be significant genes defined by some...

Hi, hum, normally that happens when `colData(dds)['station']` is not a factor. can you check what `class(colData(dds)['station'])` is giving to you?

Hi, thank you for reporting this issue. Can you tell me what version are you using? As well, how many genes are you input? More than 3K could make things...

Good question, the answer is at the beginning of the Details section. Short, it is the mean across replicates. A little longer description: ``` Before calculating the genes similarity among...

Hi Dough, You are right, I am not using scale to normalize within the sample but across sample for each gene. The idea is to be able to plot genes...

mm, actually, correlation of that example is 1, because correlation looks for same changes independently of the total value: ``` > cor.test(c(10,20,30,40), c(1010,1020,1030,1040)) Pearson's product-moment correlation data: c(10, 20, 30,...

(sorry if you got a long email, I copied a full of R code that wasn't need it, you can come to the web page to read the fixed comment)

no worries, every analysis is different and it is good to know exactly what is happening. I always try to put all the information in the docs, but it needs...