User: mzillur

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mzillur0
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Posts by mzillur

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Normalized count in edger
... Hello there, How can we find the normalized count from the count data in edger? It seems there are two opposite ways to derive normalized count from the count data. 1. normalized counts=counts*norm.factor 2. normalized counts=counts/norm.factor Which one is right? Best Regards Zillur ...
edger written 19 days ago by mzillur0 • updated 18 days ago by theodore.georgomanolis0
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Comment: C: ENSEBL gene_ID in edgeR analysis
... Thank you very much for your quick response. I have managed to overcome this problem. Your suggestions helped me a lot. I am facing another problem. I m getting totally opposite results using glmQLFit, glmQLFTest in place of glmFit and glmLRT for same contrasts. Which method I need to use to see dif ...
written 3 months ago by mzillur0
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ENSEBL gene_ID in edgeR analysis
... Hello there, I have a count file containing 50 human samples. The gencode gtf file was used to map the reads. STAR was used to map and featureCounts was used to generate count data. So, the rownames in my files are ensenbl gene_ids which looks like: `"ENSG00000231251.1" "ENSG00000236335.1" "ENSG00 ...
edger refseq enembl written 3 months ago by mzillur0 • updated 3 months ago by Gordon Smyth37k
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Comment: C: DESeq2; loading htseq-count output; sample condition is described in a different
... Thank you. My bad! Its working. Many many thanks again. Best Regards, Zillur ...
written 4 months ago by mzillur0
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Comment: C: DESeq2; loading htseq-count output; sample condition is described in a different
... Thank you. It turns out that one of my samples has zero for all genes. After removing that particular sample, its ok. Now I am having another problem in downstream analysis aka plotting. > plotCounts(d4,gene=which.min(d4$padj),intgroup = 'condition') Error in (function (classes, fdef, m ...
written 4 months ago by mzillur0
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Comment: C: DESeq2; loading htseq-count output; sample condition is described in a different
... Thank you. I have managed to load the dataset. Now facing another problem. DESeq(dds) estimating size factors Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, : every gene contains at least one zero, cannot compute log geometric means I have tried `dds=dds ...
written 4 months ago by mzillur0
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DESeq2; loading htseq-count output; sample condition is described in a different csv file
... Hello there, I have 32 samples without any string 'treated' or something like this. File names are the sample names. In another csv file I have information about those count files (case/control). How can I load these files for differential expression analysis. In the vignettes, they used 'grep' and ...
deseq2 written 4 months ago by mzillur0 • updated 4 months ago by Michael Love24k

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