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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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error when using filterFeatures #61

Closed Axe2Ash closed 6 months ago

Axe2Ash commented 6 months ago

Hi, I am new to scp and got an error when using it. I follow these tutorials: 1)https://bioconductor.org/packages/release/bioc/vignettes/scp/inst/doc/advanced.html#4_Modify_the_feature_annotations 2)https://uclouvain-cbio.github.io/SCP.replication/articles/brunner2022.html

I want to only use a subset of proteins from my dataset for statistics and added a column named "cycle" from a list of proteins of interest (follow tutorial 1). Proteins of interest have values 1.1, others are zeroes. the "cycle" column is in the same location as the column "mean" and "detected" from the filter protein section in tutorial 2. But when I tried to filter out proteins, I got "Error in rowSums(out) : 'x' must be numeric"

Coul you help me to fix this? Thanks Arthur Capture

lgatto commented 6 months ago

Difficult to say where the error comes from.

What class is Evosample of? Could you confirm it is a QFeatures. How many assays is it composed of? And do all, some or only 1 have the cycle variable?

I will have a look if you are able to share the object.

lgatto commented 6 months ago

To give you some hints as to where this error could come from, it is located in code that check the occurence of the variable you want to filter on, here cycle in the assay/set in the QFeaturesobject, here Evosample (but waiting for confirmation).

lgatto commented 6 months ago

I think I know what is happing - could you delete the cycle variable in your working environment.

lgatto commented 6 months ago

I'm am pretty sure that this is the issue (which isn't trivial to fix globally).

I'm closing this issue, but feel free to open it again in case simply rm(cycle) doesn't fix the problem.