Entering edit mode
Hello, I was wondering if you could provide any suggestions to approach this warning message (the last few sentences of the console)
I would massively appreciate any help, thank you!
# counts <- estimateCellCounts(rgSet, compositeCellType = "Blood", processMethod = "auto", probeSelect = "auto", cellTypes = c("CD8T","CD4T", "NK","Bcell","Mono","Gran"), referencePlatform = c("IlluminaHumanMethylation450k"), returnAll = FALSE, meanPlot = FALSE, verbose = TRUE)
# [estimateCellCounts] Combining user data with reference (flow sorted) data.
[estimateCellCounts] Processing user and reference data together.
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing.
[estimateCellCounts] Picking probes for composition estimation.
[estimateCellCounts] Estimating composition.
Warning messages:
1: In DataFrame(sampleNames = c(colnames(rgSet), colnames(referenceRGset)), :
'stringsAsFactors' is ignored
2: In .getSex(CN = CN, xIndex = xIndex, yIndex = yIndex, cutoff = cutoff) :
An inconsistency was encountered while determining sex. One possibility is that only one sex is present. We recommend further checks, for example with the plotSex function.
Sorry, I'm a student so some of these questions may seem trivial.
I am putting into the console the following code:
and of course, it is returning this error message (I understand I have input the wrong code, but I don't understand what to input for id as my column in my sample sheet is titled 'gender' with each patient marked as 'male' or 'female'.
if you had any guidance I would be very thankful, my apolgoies.
I understand that the id is text used as plotting symbols for y/xMed
There are two issues here. First, you get a warning about the sex check that is part of
preprocessQuantile
, and second, when you try to plot the predicted sex data, you get an error because you are missing one or more of the required items in yourcolData
object.The first question to ask yourself is do you really care about that? I mean, maybe you have all female subjects, or maybe there is a mixture, but in the end that might not be something you need to know or care about. If you do care, then you might want to move forward with figuring out what the problem is.
If you do care, do note that estimating the sex is a very simple process. Here is the code
The basic idea is to get the copy number data, subset that to the X and Y chromosomes, and then use
kmeans
to cluster into groups. You could doAnd step through the
.getSex
function and inspect thekmeans
cluster values, as well as sex0 and sex1. But again, is this critical for your analysis, and do you have only one sex?