values (NA) in p value Deseq2 (reopen)
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Entering edit mode
@8e20af93
Last seen 8 weeks ago
Colombia

Hello how are you? I reopen this question because the following has happened:

I am doing a differential expression exercise using the hisat2, stringie & DESeq2 workflow. Finally I use the python prepDE.py script recommended in the StringTie manual to extract the counts.

So far so good, I have rows of genes and columns with cases (controls and patients) with number of counts. Now, when using Deseq2 when establishing the differential expression with nbinomWaldTest, I get results in p value with (NA). The question that I was reading forums why these boxes appear with NA values ​​and they tell us that:

• If within a row, all samples have zero counts, the baseMean column will be zero, and the log2 fold change estimates, p-value, and adjusted p-value will be set to NA.
• If a row contains a sample with an extreme count outlier, the p-value and the adjusted p-value will be set to NA. These outliers are detected by Cook's distance.
• If a row is filtered by independent automatic filtering, having a low mean normalized count, only the adjusted p-value will be set to NA.

It is suggested that as filters are deactivated as follows:

res <- results (dds, cooksCutoff = FALSE, independentFiltering = FALSE)

However, in doing so I still have boxes with NA, I really don't know what I'm doing wrong and I hope someone can help me.

I share the script that I have use.

library("DESeq2")
expression_data$X <- NULL dim(expression_data) summary(expression_data) apply(expression_data, 2, sum) mx = apply( expression_data, 1, max ) expression_data = expression_data[ mx > 227, ] condition <-factor(c("control","control","paciente","paciente","paciente","paciente","paciente","paciente","paciente","paciente","paciente","paciente"),c("control","paciente")) col_data = data.frame(condition) dds = DESeqDataSetFromMatrix(expression_data, col_data, ~condition) dds = estimateSizeFactors(dds) dds = nbinomWaldTest(dds) dds <- DESeq(dds, minReplicatesForReplace=Inf) res <- results(dds, cooksCutoff=FALSE, independentFiltering =FALSE) res = results(dds) head(res) res$padj = ifelse(is.na(res$padj), 0.1, res$padj)

pvalue NA R DESeq2 • 179 views
0
Entering edit mode
@8e20af93
Last seen 8 weeks ago
Colombia

I think my mistake is due to this ... (O.o)

dds = nbinomWaldTest(dds)