User: Ld_60

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Ld_6030
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Posts by Ld_60

<prev • 12 results • page 1 of 2 • next >
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STAR and HTSeq command line parameters for 3' mRNA-Seq data
... Hi everyone, I am looking for a data analysis pipeline specifically for RNA-Seq data obtained from 3' mRNA-Seq assays (i.e. only the 3' end of the fragmented transcript is sequenced). Particularly, I would like to know which STAR (for the alignment step) and HTSeq (for the quantification step) para ...
htseq next-gen star rna-seq sequencing written 6 weeks ago by Ld_6030 • updated 6 weeks ago by michael.ante3.2k
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PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset
... Hi, I am wondering in which normalisation format (RPKM, FPKM, TPM,... etc) the PanCanAtlas EBPlusPlus-corrected RNA-seq TCGA dataset (the **EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv** file available [here][1]) is in? I know it is batch-corrected, but I don't know in which normalisati ...
ebplusplus tcga gdc rna-seq written 10 weeks ago by Ld_6030 • updated 29 days ago by user3188840
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Comment: C: GDC TCGA: cannot find CNV files by their UUIDs
... Hi Kevin, thanks a lot for your answer. I've actually found out that the CNV data has been updated in June 13th 2018 as part of the 12.0 Data Release. In the [corresponding release notes][1], the following is stated: "Updated Copy Number Segment and Masked Copy Number Segment files are now available ...
written 5 months ago by Ld_6030
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GDC TCGA: cannot find CNV files by their UUIDs
... Hi everyone, I am trying to find the corresponding TCGA sample IDs for a set of DLBC tumour samples of CNV data (downloaded in May 2018) using their file UUIDs. I am using the code provided [here][1]. The problem is that the function described in that link returns an empty table, i.e. the UUIDs of ...
uuid tcga gdc cnv written 5 months ago by Ld_6030 • updated 5 months ago by RamRS21k
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Comment: C: How to find cutoff values for gene filtering of Affymetrix microarray data
... Many thanks for your response! ...
written 9 months ago by Ld_6030
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Comment: C: How to find cutoff values for gene filtering of Affymetrix microarray data
... Hi Kevin, thanks for your reply. Indeed, I think filtering the genes is quite important in my case as my goal is to perform classification (predicting recurrence/no recurrence outcomes among cancer patients). So, selecting "potential" genes through the filtering step would be beneficial both computa ...
written 9 months ago by Ld_6030
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How to find cutoff values for gene filtering of Affymetrix microarray data
... Hi everyone, I am trying to filter out "unimportant" genes from an Affymetrix microarray dataset using gene filtering methods (filtering by coefficient of variation, by intensity values,... etc), but as these methods require cutoff values to be specified (thresholds), I was wondering how I can find ...
gene gene filtering microarray affymetrix written 9 months ago by Ld_6030 • updated 8 months ago by Biostar ♦♦ 20
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Gene filtering in microarray data normalized with the SCAN method
... Hi everyone, I am working with affymetrix microarray data, and I am willing to apply the SCAN (Single-Channel Array Normalization) method to normalize the data, as I want the normalization to be applied to individual samples instead of a batch of arrays. I am wondering which type of gene filtering ...
gene normalization gene filtering microarray scan written 9 months ago by Ld_6030
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Comment: C: GEO Affymetrix microarray datasets: how are series matrix files obtained from CE
... Hi, thank you very much for your answer, I will check that out! ...
written 9 months ago by Ld_6030
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GEO Affymetrix microarray datasets: how are series matrix files obtained from CEL files?
... Hi everyone, I am working with microarray data from the GEO repository. I am trying to understand how to obtain the feature-sample matrix format, which is represented by the directly available "series matrix" file in GEO, from the CEL files (Affymetrix platforms)? For example, considering the GPL9 ...
geo probes probe sets microarray cel written 9 months ago by Ld_6030

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