Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

[whitneyt1]

Hello!

I am trying to run DEG function with method="DESeq2" between three groups for single cell RNA seq data.

deg_BcellsM<-DEG(data %>% filter(cell_type=='B-cells-M'),method='DESeq2',contrast=c("grouped_pd","grouped_pr","naive")) but am getting the following output:

Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

My data file contains the columns as gene names + cell_type and compare_group columns, and the rows are each individual single cell. My groups are named 'grouped_pr', 'grouped_pd', 'naive'.

Do you have any advice on how to proceed?

Thank you!

[ywang65]

It seems like your input data are not integers. While DESeq2 requires raw counts as input. You can find more info about DESeq2 here https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf

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From: whitneyt [email protected] Sent: Wednesday, April 22, 2020 12:44:56 PM To: Coolgenome/iTALK Cc: Subscribed Subject: [Coolgenome/iTALK] Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers (#15)

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Hello!

I am trying to run DEG function with method="DESeq2" between three groups for single cell RNA seq data.

deg_BcellsM<-DEG(data %>% filter(cell_type=='B-cells-M'),method='DESeq2',contrast=c("grouped_pd","grouped_pr","naive")) but am getting the following output:

Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Found more than one class "DataFrame" in cache; using the first, from namespace 'PythonEmbedInR' Also defined by ‘S4Vectors’ Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are not integers

My data file contains the columns as gene names + cell_type and compare_group columns, and the rows are each individual single cell.

Do you have any advice on how to proceed?

Thank you!

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