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The signal intensities of 28,686 transcripts represented in the microarray were plotted against the RPKM values of corresponding transcripts (Supplementary Fig. S2).
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The fold-change by microarray was plotted against the fold change by RNA-Seq with an overall very strong correlation (r2 = 0.89, Figure 7A; Additional file 1, Table S5).
The expression ratios obtained from RT-qPCR and microarrays were plotted for comparison.
For each gene, mean log2 ratios (infected/control) determined by microarrays were plotted against mean log2 ratios (infected/control) determined by qPCR assays.
The ranked transcript dataset derived from our kinetic microarrays was plotted against the ARED database version 3.0 [33] that is comprised of genes reported to have functional AU-rich sequence elements in their 3'-UTR.
The expression levels of all probe sets represented on individual microarrays was plotted on a scatter graph (Figure 1A) and shows the overall pattern of differences in gene expression.
The expression data from both the apple and tomato microarrays was plotted for several of the genes identified.
Resultant data collected for each spot on the hybridized microarrays was plotted on a graph, with values from scrapie infected samples on one axis, and values from mock-infected mice on the other axis.
The bin-wise averages of log2 intensity ratios (nucleosomal DNA/genomic DNA) in the given window from microarray data were plotted against the distance from the reference point (TSS or TTS).
When the microarray and qPCR outputs were plotted against each other and matched gene for gene across the patients, the overall correlation was r = 0.60 (Fig. 1).
Average expression values from microarray and RT-qPCR data were plotted for each developmental stage.
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