10x data formatting

[kathirij]

hello,
This is a rather basic question. I am trying to upload the matrix (.mtx) file that is an output of the cellrangerRkit.

"gbm_cds <- newCellDataSet(exprs(gbm),
phenoData = new("AnnotatedDataFrame", data=pData(gbm)),
featureData = new("AnnotatedDataFrame", data=fData(gbm)),
lowerDetectionLimit = 0.5,
expressionFamily = negbinomial.size())"

However, the matrix does not have the correct featureData. I get the error:

"none of your featureData columns are named “gene_short_name”. Some functions will not be able to take this function as an input as a result"

Do I need to change a column title [that is currently labeled as "symbol"] to "gene_short_name"? If not, will it create problems when I run some of the downstream analyses? For example when I calculate dispersions or when I classify cell type hierarchy?

Also,featureData of my matrix looks like this:

> fData(gbm)
                      id                       symbol
ENSMUSG00000051951 ENSMUSG00000051951           Xkr4
ENSMUSG00000089699 ENSMUSG00000089699         Gm1992
ENSMUSG00000102343 ENSMUSG00000102343        Gm37381
ENSMUSG00000025900 ENSMUSG00000025900            Rp1

[ctrapnell]

Yes, we recommend changing the “symbol” column to “gene_short_name” in the featureData table. Cole Trapnell Assistant Professor Department of Genome Sciences University of Washington http://cole-trapnell-lab.github.io/ On Fri, May 19, 2017 at 1:11 PM kathirij < mailto:kathirij <notifications@github.com> > wrote: a, pre, code, a:link, body { word-wrap: break-word !important; } hello, This is a rather basic question. I am trying to upload the matrix (.mtx) file that is an output of the cellrangerRkit. "gbm_cds <- newCellDataSet(exprs(gbm), phenoData = new("AnnotatedDataFrame", data=pData(gbm)), featureData = new("AnnotatedDataFrame", data=fData(gbm)), lowerDetectionLimit = 0.5, expressionFamily = negbinomial.size())" However, the matrix does not have the correct featureData. I get the error: "none of your featureData columns are named “gene_short_name”. Some functions will not be able to take this function as an input as a result" Do I need to change a column title [that is currently labeled as "symbol"] to "gene_short_name"? If not, will it create problems when I run some of the downstream analyses? — You are receiving this because you are subscribed to this thread. Reply to this email directly, #27 , or https://github.com/notifications/unsubscribe-auth/AAR_GWHZJScp3vmxkvJ_B4nYrqK2rYXeks5r7fdYgaJpZM4Ng9ud .

[Xiaojieqiu]

this is the same issue as in #24 . I will close it now. please refer to the other issue. meanwhile, the monocle 2 website will be updated to incorporate those info