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 12 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 12 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 12 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 12 months ago by kaur0 • updated 12 months ago by Gordon Smyth39k

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