User: kaur

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kaur0
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Posts by kaur

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Comment: C: Count filter for differential expression
... Thank you so much for this information!! I feel very lucky to get advise directly from somebody who developed these packages.  While we use R to plot the data (heatmaps, volcano plots, circos…), we have performed the differential analysis on usegalaxy.org 😊 Here, we have to specify whether we filt ...
written 3 months ago by kaur0
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Comment: C: Count filter for differential expression
... The results fit better means we have data on RNA and protein level of many genes from experimental work already (PCR and ELISA).  Applying a filter lets us reproduce the PCR and ELISA data, whereas doing differential analysis without any count filter only partially shows what we have seen with PCR ...
written 3 months ago by kaur0
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Comment: C: Count filter for differential expression
... We are comparing wildtype to knock out cells. We have three replicates per condition. We filtered with average expression across the three replicates bigger x in either condition as a criterium. For picking the value x we took the following into consideration: count number for the gene that is k ...
written 3 months ago by kaur0
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Count filter for differential expression
... Hi! We received NGS data from a payed facility which performed differential expression analysis without filtering out low expressing genes (mouse, FC calculated for ~50.000 genes) Now we re-analyzed the data with two different filters (tried limma and edgeR): (1) Raw counts > 10 which left us ...
limma edger counts written 3 months ago by kaur0 • updated 3 months ago by Gordon Smyth36k

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