User: lirongrossmann

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Posts by lirongrossmann

<prev • 46 results • page 2 of 5 • next >
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Deseq2 for small matched samples
... Hi everyone, I have 16 rna seq samples (not replicates) and I want to compare 8 vs 8 which are paired matched. Are there any adjustments when using Deseq I can make for the small sample size and pairwise comparisons? Thanks! ...
deseq2 written 5 months ago by lirongrossmann10 • updated 5 months ago by Michael Love17k
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Comment: C: calculating logfold change from variance stabilizing transformation
... Thank you so much!  I see that SamSeq requires normalized data to run. From your experience, is it “safe” to give SamSeq the output of variance stabilizing transformation from Deseq2 as the input for the analysis. ...
written 5 months ago by lirongrossmann10
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Comment: C: calculating logfold change from variance stabilizing transformation
... My groups are small (9 vs 9 samples) and for some reason when I tried a different statistical test to compare them (Wilcoxon rank sum test, to be specific), I got a more uniform expression within each group for the genes that were significant. When I used Deseq to perform the statistical test, the g ...
written 5 months ago by lirongrossmann10
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calculating logfold change from variance stabilizing transformation
... Hi All, I am interested in calculating the logfold change from the transformed expression file obtained by using variance stabilizing transformation function.  I used the transformed data to normalize my count data and compare two groups within the data using a different statistical test than the ...
deseq2 variancestabilizingtransformation logfoldchange written 5 months ago by lirongrossmann10 • updated 5 months ago by Michael Love17k
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Comment: C: comparing strand-specific counts to unstranded counts
... thank you!  My goal is to choose the genes that best discriminate my two groups in terms of their response to the treatment and use them for downstream analysis.  Since I have a batch effect confounding the biological effect (response to treatment) I am not sure which genes to choose based on the ...
written 5 months ago by lirongrossmann10
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Comment: C: comparing strand-specific counts to unstranded counts
... Thank you. I think that what confuses me is how to interpret the overall result of which gene can be a good candidate to discriminate between the two groups I have from a biologic standpoint.  To be more specific - I have two groups, each has 10 samples. One group responded to therapy the other di ...
written 5 months ago by lirongrossmann10
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Comment: C: comparing strand-specific counts to unstranded counts
...  Thanks!  So basically it accounts for the batch in a linear fashion if it uses GLM.   ...
written 5 months ago by lirongrossmann10
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Comment: A: comparing strand-specific counts to unstranded counts
... Thanks! Does Deseq2 treat the batch effect as a linear covariate or does it take into account non linear variations that the batch may include? ( I.e other than an offset) ...
written 5 months ago by lirongrossmann10
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Comment: C: Quantile normalization and Deseq2
... Thanks, I just wanted to make sure that genes that have "low" counts in two samples are comparable (i.e. have similar rank for example). ...
written 5 months ago by lirongrossmann10
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Quantile normalization and Deseq2
...  Hi all, I am using variance stabilizing transformation on my rna seq count data with Deseq2. Do I need to use quantile normalize the samples or does variance stabilizing transformation function take care of it?   ...
deseq2 quantile normalization written 5 months ago by lirongrossmann10 • updated 5 months ago by Michael Love17k

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