User: sujitsilas

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Posts by sujitsilas

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Comment: C: RNA-Seq Data analysis
... Thank you for your insight! ...
written 5 weeks ago by sujitsilas0
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Comment: C: RNA-Seq Data analysis
... Thank you! I'll look into that. I also have a .csv file format of the same experiment with FPKM data. Can the FPKM data be used in any way to find differentially expressed genes between the two datasets? ...
written 5 weeks ago by sujitsilas0
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Comment: C: RNA-Seq Data analysis
... But is there a way to look at the differences in gene expression between the two days? I also have a .csv file format of the same experiment with FPKM data. Can the FPKM data be used in any way? ...
written 5 weeks ago by sujitsilas0
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RNA-Seq Data analysis
... Hello everyone, I had tried comparing two gene expression datasets in the .tsv file formats (reads quantified using Salmon) that were obtained from the RefineBio website. I was able to annotate the data using Galaxy using a GTF file from ENSEMBL, but when I tried using edgeR or limma, an error would ...
.tsv fpkm volcano plots salmon rna-seq written 5 weeks ago by sujitsilas0 • updated 5 weeks ago by dsull1.8k
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Comment: C: GEO Accession transcriptome data comparison with custom gene expression sets
... I believe It’s going to be more like a meta-analysis. The p values and the fold change data would be more than enough to identify new candidates. However, I am not sure how each of the dataset can be normalized independently before comparison. I had tried using fold change functions but was unsure i ...
written 7 weeks ago by sujitsilas0
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Comment: C: GEO Accession transcriptome data comparison with custom gene expression sets
... Thank you for the insight, Kevin !! The ultimate goal is to compare these datasets to another experimental transcriptome dataset (given to me by my professor). The goal is to find new candidate genes that overlap with genes expressed in ectoderm or neuroectoderm development, and establish if there a ...
written 7 weeks ago by sujitsilas0
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Comment: C: GEO Accession transcriptome data comparison with custom gene expression sets
... ![This is how the data in the .csv file looks like: link: https://ibb.co/Cw56j8c ...
written 7 weeks ago by sujitsilas0 • updated 7 weeks ago by Kevin Blighe70k
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Comment: C: GEO Accession transcriptome data comparison with custom gene expression sets
... GSE107552 GSE103715 GSE147270 ...
written 7 weeks ago by sujitsilas0
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GEO Accession transcriptome data comparison with custom gene expression sets
... Hello, I had recently downloaded transcriptome data sets from GEO archive. I am trying to compare them to custom experimental datasets to find overlapping genes and differentially expressed genes. I previously tried using the supplementary files, the .soft files, the GEOquery package to access the ...
geo R deseq2 rna-seq transcriptome written 7 weeks ago by sujitsilas0

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