Deseq2

[luana]

Hello guys,

I need to run Deseq2, but when I try to run this part of command the following error message appears.

dds <- DESeqDataSetFromMatrix(countData = countData,
+ colData = design,
+ design = ~ condition)

Error in DESeqDataSet(se, design = design, ignoreRank) :
NA values are not allowed in the count matrix


I've looked at my table but don't have NA values.
What can I do to solve?

thanks!

[fanli]

Well, that seems as clear an error message as can be. Since we can't see your dataset, can you verify with output from:

any(is.na(countData))
all(is.numeric(countData))

[luana]

The problem is when I put a table with 22480 genes at end Deseq2 gives me a table with 16668 genes, 5000 genes are cut.
And when I try to run this part
dds <- DESeqDataSetFromMatrix(countData = countData,
colData = design,
design = ~ condition)

this mesage appears
Error in DESeqDataSet(se, design = design, ignoreRank) :
NA values are not allowed in the count matrix

I tried your command fanli, but didn't work

I don't know how to fix this!

[Persistent LABS]

The problem is when I put a table with 22480 genes at end Deseq2 gives me a table with 16668 genes, 5000 genes are cut.
And when I try to run this part
dds <- DESeqDataSetFromMatrix(countData = countData,
colData = design,
design = ~ condition)

this mesage appears
Error in DESeqDataSet(se, design = design, ignoreRank) :
NA values are not allowed in the count matrix

I tried your command fanli, but didn't work

I don't know how to fix this!

The error message suggests that your countData table has NA values. To confirm it, fanli has suggested to share the output of the two commands. Please share the output.