TPM value from DESE2 and significant filterig isssue

Question

[Nai]

The code 10101 res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2FoldChange <numeric> <numeric> DDX11L1 1.779144 -1.4955939 WASH7P 152.518293 -0.0505911 MIR6859-1 20.653876 0.5689275 MIR1302-2HG 0.255387 -1.9691031 FAM138A 0.353478 0.1574042

Then I will get rownames: 1 (Output of : subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1)

  baseMean       log2FoldChange        lfcSE          stat                 pvalue                   padj

ZWINT 82.3486 -1.74934 0.330334 -5.29568 1.18575e-07 0.0043631

By using subset and filtering of padj and logfold , I did not get significant result. How can I get TPM group 1 and group 2 value for each gene

[ATpoint]

Hi, could you please reformat this post using the code 10101 option to highlight code and data?

[Nai]

Where I have to mention the code 10101

[bigomics.team]

Is your question how to get the average TPM of group1 and group2? From the output it would be group1_avg=2^(-1.749/2)*82.35 and group2_avg=2^(+1.749/2)*82.35. Because the average was done in the logarithm (I presume), it is a geometric average.

[ATpoint]

TPM is counts, what the DESeq2 results table bas is fold changes and baseMean, and the baseMean is the rowMean for every gene (so across all samples in the count matrix). If you want TPM (or any count unit) then you have to go and extract that from the results. @OP, can you please reformat your post, it is messy and (at least me) have a hard time even understanding what the problem is. Select code with the mouse, then press the code button in the format bar on top of the comment/answer box.

[Nai]

group1_avg=2^(-Logfoldchange/2)basemean and group2_avg=2^(+logfoldchnage/2)basemean

Why are we calculating exponential . Any body please explain!

[Nai]

My file has values of baseMean log2FoldChange lfcSE stat pvalue padj. I don't have TPM values. How I can I analyzed in DeSeq2 or any other tool. To get TPM values.

1. When I am putting criteria for significant search (subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1 on the file which have baseMean , log2FoldChange, lfcSE , stat , pvalue , padj. Then I am getting only one gene row.

[ATpoint]

If you do not have counts you cannot get TPMs, simple as that. That information is lost in the results table.

[Nai]

I have counts data after that I got 36000 genes. Out of these I wanted to separate significant genes with the command (subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1. I have no idea how to generate TPM data using counts or deseq2 results

[ATpoint]

DESeq2 has many functions to create normalized counts, please see the manual.

#/ normalized counts:
counts(dds, normalized=TRUE)

#/ normalized counts on log2 scale:
log2(counts(dds, normalized=TRUE)+1)

#/ variance stabilized (preferred method) on log-like scale:
vst(dds)

#/ normalized and regularized on log2 scale:
rlog(dds)

#/ fpkm:
fpkm(dds)

#/ fpm:
fpm(dds)

TPM is not directly supported, just use FPKM if you want length-corrected counts.

[Nai]

Hopefully by these commands, i will get desired output. Then update you.