User: affy snp

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affy snp640
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Posts by affy snp

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Up- or down- regulated pathways or GO terms?
... Hi all, I wonder whether there is any tool which can demonstrate up- or down- regulation of pathways or GO terms in a plot when doing microarray analysis? Thanks a lot! Allen [[alternative HTML version deleted]] ...
microarray pathways go written 10.3 years ago by affy snp640 • updated 10.3 years ago by Paolo Sonego140
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Convert KEGGpathway to nuID in lumi
... Dear all, I'd appreciate your input if you could. I first normalized data, and it is called john2. We are interested in Notch signaling pathway and want to get the expression values for all genes on this pathway. So I tried the below (it does not look neat...sorry that I am new to R coding): ###### ...
written 10.4 years ago by affy snp640 • updated 10.4 years ago by Martin Morgan ♦♦ 23k
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Comment: C: About GEO submission of Illumina data by lumi
... Hi Pan, I have tried the code you provided and got the submissionFile like: #ID_REF = #VALUE = normalized signal intensity #RAW_VALUE = raw signal intensity #BEAD_STDERR = the standard error of the probe measurements #Detection_Pval = the detection p-value of the probe #Avg_NBEADS = Number of bead ...
written 10.4 years ago by affy snp640
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Comment: C: About GEO submission of Illumina data by lumi
... Hi Pan, Thanks so much. Just a little bit updates for you by our conversations with folks in GEO. They suggest that the platform needs to be in the same file of submissionFile as the samples+series (as a family with all three entities), like this: http://www.ncbi.nlm.nih.gov/projects/geo/info/so ...
written 10.4 years ago by affy snp640
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Comment: C: About GEO submission of Illumina data by lumi
... Hi Pan, Obviously I am writing back to you again for help. A lot of hurdles have been cleared by working with folks in GEO except that the IDs in the platform table are not unique. ID Illumina_ProbeID Illumina_Gene lumiID Search_Key Accession Symbol ProbeSequence ILMN_30605 1 ...
written 10.4 years ago by affy snp640
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Comment: C: About GEO submission of Illumina data by lumi
... Thank you, Pan. I am grateful to your help! So for the new platform, I can basically use the one generated by produceGEOPlatformFile? Regards, Allen On Thu, Feb 26, 2009 at 4:28 PM, Pan Du wrote: > That is a problem of Illumina platform. The probe number might be > different across ...
written 10.4 years ago by affy snp640
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Comment: C: About GEO submission of Illumina data by lumi
... Thanks, Pan for the help. Unfortunately, there are 46,713 rows in my data which is less than 46, 718 rows of the platform GPL6790. So GEO detected this as error: .... The data table of "FOM173/Nic-rep2" has 46713 ID_REFs out of a possible 46718. Your submission has failed MIAME validation. But I ...
written 10.4 years ago by affy snp640
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Comment: C: About GEO submission of Illumina data by lumi
... *Dear Sean,* ** You are absolutely right. ID_REF in my submission file does not match IDs in GPL6790, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6790. The first two rows in my submission file look like: ID_REF nuID VALUE RAW_VALUE BEAD_STDERR Detection_Pval Avg_NBEADS 0006960451 NQqs8dKR ...
written 10.4 years ago by affy snp640
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Comment: C: About GEO submission of Illumina data by lumi
... Hi Pan, I guess I see what the problem might be. The platform I picked, Platform GPL6790, available at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6790 has all its ID like ILMN_89282, starting with "ILMN_". However, in my GEOSubmissionFile, the "ID_REF" column is: 0006960451, 0002850504 ...
written 10.4 years ago by affy snp640
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Comment: C: About GEO submission of Illumina data by lumi
... Hi Pan, Thanks much! I did manually fill up the blanks in the sampleInfo otherwise GEOSubmissionFile would not be generated. You are right about the platform ID (I picked one, updated the sampleInfo file and submitted the GEOSubmissionFile again). Now I got the error as: Error: At line #27, Inval ...
written 10.4 years ago by affy snp640

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