User: andorjkiss

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andorjkiss10
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1 week ago
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4 years, 9 months ago
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Posts by andorjkiss

<prev • 11 results • page 1 of 2 • next >
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Comment: C: What kind of Affymetrix SNP 6.0 datafile is this?
... Okay, I've found the CEL files, the CHP files and studied how to do this via Bioconductor in R. I think that the RMA has been done and might already be in the CHP file(s). However, in the event that I need to normalise myself, I would have to choose an appropriate database file for the normalizati ...
written 25 days ago by andorjkiss10
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Comment: C: What kind of Affymetrix SNP 6.0 datafile is this?
... Okay, thanks - this is very helpful. What we're ultimately trying to do is to use a programme called "InFlo" that makes use of datasets (RNA-Seq; WGS; WXS; SNP; Methylation) to build network maps. So, their input example file (https://github.com/VaradanLab/InFlo) is apparently L3 RMA Normalised (h ...
written 4 weeks ago by andorjkiss10
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Comment: C: What kind of Affymetrix SNP 6.0 datafile is this?
... Sure, it's from the Osteosarcoma public data set at TARGET: https://ocg.cancer.gov/programs/target/data-matrix ...
written 5 weeks ago by andorjkiss10
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Comment: A: What kind of Affymetrix SNP 6.0 datafile is this?
... So this is un-normalised data, correct? And if I wanted normalised data (say L3 RMA-normalised) I would have to obtain the CEL/CDF files? Am I correct about this for normalisation? TIA ...
written 5 weeks ago by andorjkiss10
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What kind of Affymetrix SNP 6.0 datafile is this?
... Hi, I'm new to microarray data formats and I'm wondering exactly what state this data is in (normalised?, CEL (txt version)? It's publically available data from the Osteosarcoma study from NCI TARGET. It's Affymetrix SNP 6.0 (human). TIA Example here: SampleName ...
snp 6.0 affymetrix written 5 weeks ago by andorjkiss10
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Answer: A: How do you interpret the results from GSEA analysis in CLC Genomics workbench?
... There's a section in the manual that explains how the GSEA test is implemented: http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/780/index.php?manual=Gene_set_enrichment_analysis.html Conceptually, the entry to wikipedia (https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis ...
written 9 months ago by andorjkiss10
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Comment: C: How to analyse RNA-Seq data with JUST geneID and TPM values
... Yeah, thanks - this is also my feeling - without the FASTQ, we're (I'm) making a lot of assumptions - especially with isoforms and potential non-unique fragment mappings (I didn't analyse the data initially). Thanks All. ...
written 15 months ago by andorjkiss10
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Comment: C: How to analyse RNA-Seq data with JUST geneID and TPM values
... Okay, thanks for the tip on DESeq2. Further to this discussion, if one has the output of SAMSeq (R smar), is there a means to easily visualise this data? I have the following in tabular data (gene_ID; mean_length; mean_eff_length; est_counts; tpm) for disease/non-disease states. ...
written 16 months ago by andorjkiss10
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Comment: C: How to analyse RNA-Seq data with JUST geneID and TPM values
... Thanks, I'll check it out. But my sense of DESeq2 is that one needed the total counts... ...
written 16 months ago by andorjkiss10
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How to analyse RNA-Seq data with JUST geneID and TPM values
... Hi, I have a spreadsheet with the geneIDs and the TPM values only. Is there any software that will analyse this in terms of Differential Gene Expression, possibly GO? Or is this pretty much just a big laundry list? Thanks, Andor ...
geneid tpm rna-seq dge written 16 months ago by andorjkiss10 • updated 16 months ago by igor8.1k

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