User: david.peeney

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david.peeney20
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Posts by david.peeney

<prev • 11 results • page 1 of 2 • next >
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duplicate UUIDs, yet unique legacy UUIDs (and count data) in TCGA data
... Hi I have recount2 data from breast TCGA RNA-seq. The recount2 data file IDs are TCGA legacy UUIDs. Upon converting these legacy UUIDs to harmonized UUIDs, there are 5 duplicate aliquot UUIDs and aliquot barcodes (after exclusion of FFPE samples). for example: legacy UUID > harmonized aliquot ...
tcga gdc rna-seq written 6 weeks ago by david.peeney20 • updated 6 weeks ago by Kevin Blighe41k
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Answer: A: Sample names for TCGA data from GDC-legacy archive
... copying my answer from [Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R][1] Using the GenomicDataCommons method only gives you short barcodes (for identifying patients), which is not particularly useful when dealing with duplicate samples. A good method I found that gives me harmonized UUIDs a ...
written 6 weeks ago by david.peeney20
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Answer: A: TCGA UUIDS to TCGA barcode (SampleID) in R
... I had a hard time getting a number of these answers to work... eventually using the following sequence to convert legacy UUIDs to full barcodes and harmonized UUIDs: Firstly, you need to download the JSON manifest files from your selected study and file types from the GDC legacy archive (NOT GDC p ...
written 6 weeks ago by david.peeney20
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Comment: C: RPKM to TPM conversion?
... hey... did you find any articles citing this equation or the validity of the TPM conversion? I am having the same issue ...
written 9 weeks ago by david.peeney20
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Comment: C: comparing RNA seq data from different studies using ratios
... This doesn't quite answer the question I am asking... I understand that the normalization techniques differ. The question is, would the ratio between gene X and gene Y significantly differ if the raw counts were processed to give us FPMK-UQ, FPKM, TPM or RSEM. ...
written 3 months ago by david.peeney20
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comparing RNA seq data from different studies using ratios
... Hi all I have a question with regards to comparison between RNA seq datasets that have been analyzed using different techniques (in this case FPKM-UQ vs TPM). For reference, the data is cBioportal harvested TCGA data (FPKM-UQ) and GTEx TPMs downloaded from the GTEx portal. I am not comparing count ...
rna-seq written 3 months ago by david.peeney20 • updated 3 months ago by rrbutleriii50
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Answer: A: issues with GTEx data annotation files
... Ok... was actually really simple. Although it never worked as a text file in excel, i converted the file to .csv in R. ...
written 3 months ago by david.peeney20
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Comment: C: issues with GTEx data annotation files
... same problem on windows. If anybody else can successfully perform the text to columns function, please let me know ...
written 3 months ago by david.peeney20
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Comment: C: issues with GTEx data annotation files
... I have tried it... For some reason excel is not recognizing the tabs. Maybe I will try excel on a windows machine ...
written 3 months ago by david.peeney20
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issues with GTEx data annotation files
... Hi all... I am having issues with obtaining sample annotation data from the GTEx dataset, specifically the origin tissue (which should be under the column "SMTSD". Spaces are used as a delimiter in the dataset, but I cannot get the data to appropriately align in excel (probably because some data poi ...
excel gtex written 3 months ago by david.peeney20

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Scholar 3 months ago, created an answer that has been accepted. For A: issues with GTEx data annotation files

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