[R] Normalize GEO Data

Matthew McCormack mccorm@ck @end|ng |rom mo|b|o@mgh@h@rv@rd@edu
Mon Aug 15 20:03:17 CEST 2022

Hi Anas,

     How many replicates were there ?  and about how many genes are 
up-regulated (>logFC 1) and downregulated (<logFC1) ? Are there any 
genes with logFC > 4 or more or < logFC 4 ?


On 8/15/22 11:34 AM, Anas Jamshed wrote:
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> I performed GEO2R analysis on a series dataset and I'm looking to find the
> up-regulated and down-regulated genes. I know that to find up-regulated and
> down-regulated genes, I should check logFC (Fold-change in log2 scale
> (generally)).Consider the value of 1 in log2 is 0. There is optimal cutoff
> but log2 > 1 indicates up-regulation and log2 < -1 indicates
> down-regulation of genes. Moreover, I should consider adj.p.val which is
> the adjusted p-value (corrected p-value dues multiple comparisons). Again
> there is no generally accepted cutoff but I should consider values < 0.05
> which indicates the test is statistically significant.
> But the problem is in this particular GSE series none of the adj.p.value is
> < 0.05 - they are all "1" and a "0.636". However, the logFC values are >1,
> but none of the samples have a condition of "p <0.05 & logFC > 1".
> So, can it be said that in this case, I need to normalise my data to find
> out the DEGs, up-regulated and down-regulated genes in a series GEO file?
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